]> git.uio.no Git - u/mrichter/AliRoot.git/blame - ANALYSIS/AliAnalysisAlien.cxx
git://git.uio.no / u / mrichter / AliRoot.git / blame
? search:
summary | shortlog | log | commit | commitdiff | tree
blob | blame (incremental) | history | HEAD
Added functionality to also process calorimeter data + some changes in cuts (Ana)
[u/mrichter/AliRoot.git] / ANALYSIS / AliAnalysisAlien.cxx
CommitLineData
c57f56b7 1/**************************************************************************
2 * Copyright(c) 1998-2007, ALICE Experiment at CERN, All rights reserved. *
3 * *
4 * Author: The ALICE Off-line Project. *
5 * Contributors are mentioned in the code where appropriate. *
6 * *
7 * Permission to use, copy, modify and distribute this software and its *
8 * documentation strictly for non-commercial purposes is hereby granted *
9 * without fee, provided that the above copyright notice appears in all *
10 * copies and that both the copyright notice and this permission notice *
11 * appear in the supporting documentation. The authors make no claims *
12 * about the suitability of this software for any purpose. It is *
13 * provided "as is" without express or implied warranty. *
14 **************************************************************************/
15
16// Author: Mihaela Gheata, 01/09/2008
17
18//==============================================================================
19// AliAnalysisAlien - AliEn utility class. Provides interface for creating
20// a personalized JDL, finding and creating a dataset.
21//==============================================================================
22
23#include "Riostream.h"
0f389141 24#include "TEnv.h"
25#include "TError.h"
c57f56b7 26#include "TROOT.h"
27#include "TSystem.h"
28#include "TFile.h"
29#include "TObjString.h"
30#include "TObjArray.h"
31#include "TGrid.h"
32#include "TGridResult.h"
33#include "TGridCollection.h"
34#include "TGridJDL.h"
d2a409b2 35#include "TGridJobStatusList.h"
36#include "TGridJobStatus.h"
c57f56b7 37#include "TFileMerger.h"
38#include "AliAnalysisManager.h"
bb885a9e 39#include "AliVEventHandler.h"
40#include "AliAnalysisDataContainer.h"
c57f56b7 41#include "AliAnalysisAlien.h"
42
43ClassImp(AliAnalysisAlien)
44
45//______________________________________________________________________________
46AliAnalysisAlien::AliAnalysisAlien()
47 :AliAnalysisGrid(),
48 fGridJDL(NULL),
0f389141 49 fMergingJDL(NULL),
c57f56b7 50 fPrice(0),
51 fTTL(0),
52 fSplitMaxInputFileNumber(0),
53 fMaxInitFailed(0),
54 fMasterResubmitThreshold(0),
bb885a9e 55 fNtestFiles(0),
319593fb 56 fNrunsPerMaster(0),
16a4353c 57 fMaxMergeFiles(0),
d2a409b2 58 fNsubmitted(0),
a3e84053 59 fProductionMode(0),
cd11251e 60 fOutputToRunNo(0),
0f389141 61 fMergeViaJDL(0),
62 fFastReadOption(0),
63 fOverwriteMode(0),
c57f56b7 64 fRunNumbers(),
65 fExecutable(),
0a1c1f7f 66 fExecutableCommand(),
c57f56b7 67 fArguments(),
631c0b05 68 fExecutableArgs(),
c57f56b7 69 fAnalysisMacro(),
70 fAnalysisSource(),
d5c6455a 71 fAdditionalRootLibs(),
c57f56b7 72 fAdditionalLibs(),
73 fSplitMode(),
74 fAPIVersion(),
75 fROOTVersion(),
76 fAliROOTVersion(),
648174cf 77 fExternalPackages(),
c57f56b7 78 fUser(),
79 fGridWorkingDir(),
80 fGridDataDir(),
81 fDataPattern(),
82 fGridOutputDir(),
83 fOutputArchive(),
84 fOutputFiles(),
85 fInputFormat(),
e7c71df0 86 fDatasetName(),
c57f56b7 87 fJDLName(),
bb885a9e 88 fMergeExcludes(),
f965131e 89 fIncludePath(),
bb885a9e 90 fCloseSE(),
0df6ccf2 91 fFriendChainName(),
c6cb3634 92 fJobTag(),
648174cf 93 fOutputSingle(),
5fce53f4 94 fRunPrefix(),
4e5c5506 95 fInputFiles(0),
96 fPackages(0)
c57f56b7 97{
98// Dummy ctor.
99 SetDefaults();
100}
101
102//______________________________________________________________________________
103AliAnalysisAlien::AliAnalysisAlien(const char *name)
104 :AliAnalysisGrid(name),
105 fGridJDL(NULL),
0f389141 106 fMergingJDL(NULL),
c57f56b7 107 fPrice(0),
108 fTTL(0),
109 fSplitMaxInputFileNumber(0),
110 fMaxInitFailed(0),
111 fMasterResubmitThreshold(0),
bb885a9e 112 fNtestFiles(0),
319593fb 113 fNrunsPerMaster(0),
16a4353c 114 fMaxMergeFiles(0),
d2a409b2 115 fNsubmitted(0),
a3e84053 116 fProductionMode(0),
cd11251e 117 fOutputToRunNo(0),
0f389141 118 fMergeViaJDL(0),
119 fFastReadOption(0),
120 fOverwriteMode(0),
c57f56b7 121 fRunNumbers(),
122 fExecutable(),
0a1c1f7f 123 fExecutableCommand(),
c57f56b7 124 fArguments(),
631c0b05 125 fExecutableArgs(),
c57f56b7 126 fAnalysisMacro(),
127 fAnalysisSource(),
d5c6455a 128 fAdditionalRootLibs(),
c57f56b7 129 fAdditionalLibs(),
130 fSplitMode(),
131 fAPIVersion(),
132 fROOTVersion(),
133 fAliROOTVersion(),
648174cf 134 fExternalPackages(),
c57f56b7 135 fUser(),
136 fGridWorkingDir(),
137 fGridDataDir(),
138 fDataPattern(),
139 fGridOutputDir(),
140 fOutputArchive(),
141 fOutputFiles(),
142 fInputFormat(),
e7c71df0 143 fDatasetName(),
c57f56b7 144 fJDLName(),
bb885a9e 145 fMergeExcludes(),
f965131e 146 fIncludePath(),
bb885a9e 147 fCloseSE(),
0df6ccf2 148 fFriendChainName(),
c6cb3634 149 fJobTag(),
648174cf 150 fOutputSingle(),
5fce53f4 151 fRunPrefix(),
4e5c5506 152 fInputFiles(0),
153 fPackages(0)
c57f56b7 154{
155// Default ctor.
156 SetDefaults();
157}
158
159//______________________________________________________________________________
160AliAnalysisAlien::AliAnalysisAlien(const AliAnalysisAlien& other)
161 :AliAnalysisGrid(other),
162 fGridJDL(NULL),
0f389141 163 fMergingJDL(NULL),
c57f56b7 164 fPrice(other.fPrice),
165 fTTL(other.fTTL),
166 fSplitMaxInputFileNumber(other.fSplitMaxInputFileNumber),
167 fMaxInitFailed(other.fMaxInitFailed),
168 fMasterResubmitThreshold(other.fMasterResubmitThreshold),
bb885a9e 169 fNtestFiles(other.fNtestFiles),
319593fb 170 fNrunsPerMaster(other.fNrunsPerMaster),
16a4353c 171 fMaxMergeFiles(other.fMaxMergeFiles),
d2a409b2 172 fNsubmitted(other.fNsubmitted),
a3e84053 173 fProductionMode(other.fProductionMode),
cd11251e 174 fOutputToRunNo(other.fOutputToRunNo),
0f389141 175 fMergeViaJDL(other.fMergeViaJDL),
176 fFastReadOption(other.fFastReadOption),
177 fOverwriteMode(other.fOverwriteMode),
c57f56b7 178 fRunNumbers(other.fRunNumbers),
179 fExecutable(other.fExecutable),
0a1c1f7f 180 fExecutableCommand(other.fExecutableCommand),
c57f56b7 181 fArguments(other.fArguments),
631c0b05 182 fExecutableArgs(other.fExecutableArgs),
c57f56b7 183 fAnalysisMacro(other.fAnalysisMacro),
184 fAnalysisSource(other.fAnalysisSource),
d5c6455a 185 fAdditionalRootLibs(other.fAdditionalRootLibs),
c57f56b7 186 fAdditionalLibs(other.fAdditionalLibs),
187 fSplitMode(other.fSplitMode),
188 fAPIVersion(other.fAPIVersion),
189 fROOTVersion(other.fROOTVersion),
190 fAliROOTVersion(other.fAliROOTVersion),
648174cf 191 fExternalPackages(other.fExternalPackages),
c57f56b7 192 fUser(other.fUser),
193 fGridWorkingDir(other.fGridWorkingDir),
194 fGridDataDir(other.fGridDataDir),
195 fDataPattern(other.fDataPattern),
196 fGridOutputDir(other.fGridOutputDir),
197 fOutputArchive(other.fOutputArchive),
198 fOutputFiles(other.fOutputFiles),
199 fInputFormat(other.fInputFormat),
e7c71df0 200 fDatasetName(other.fDatasetName),
c57f56b7 201 fJDLName(other.fJDLName),
bb885a9e 202 fMergeExcludes(other.fMergeExcludes),
f965131e 203 fIncludePath(other.fIncludePath),
bb885a9e 204 fCloseSE(other.fCloseSE),
0df6ccf2 205 fFriendChainName(other.fFriendChainName),
c6cb3634 206 fJobTag(other.fJobTag),
648174cf 207 fOutputSingle(other.fOutputSingle),
5fce53f4 208 fRunPrefix(other.fRunPrefix),
4e5c5506 209 fInputFiles(0),
210 fPackages(0)
c57f56b7 211{
212// Copy ctor.
213 fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
0f389141 214 fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
a8739e8a 215 fRunRange[0] = other.fRunRange[0];
216 fRunRange[1] = other.fRunRange[1];
c57f56b7 217 if (other.fInputFiles) {
218 fInputFiles = new TObjArray();
219 TIter next(other.fInputFiles);
220 TObject *obj;
221 while ((obj=next())) fInputFiles->Add(new TObjString(obj->GetName()));
222 fInputFiles->SetOwner();
223 }
4e5c5506 224 if (other.fPackages) {
225 fPackages = new TObjArray();
226 TIter next(other.fPackages);
227 TObject *obj;
228 while ((obj=next())) fPackages->Add(new TObjString(obj->GetName()));
229 fPackages->SetOwner();
230 }
c57f56b7 231}
232
233//______________________________________________________________________________
234AliAnalysisAlien::~AliAnalysisAlien()
235{
236// Destructor.
237 if (fGridJDL) delete fGridJDL;
0f389141 238 if (fMergingJDL) delete fMergingJDL;
c57f56b7 239 if (fInputFiles) delete fInputFiles;
4e5c5506 240 if (fPackages) delete fPackages;
c57f56b7 241}
242
243//______________________________________________________________________________
244AliAnalysisAlien &AliAnalysisAlien::operator=(const AliAnalysisAlien& other)
245{
246// Assignment.
247 if (this != &other) {
248 AliAnalysisGrid::operator=(other);
249 fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
0f389141 250 fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
c57f56b7 251 fPrice = other.fPrice;
252 fTTL = other.fTTL;
253 fSplitMaxInputFileNumber = other.fSplitMaxInputFileNumber;
254 fMaxInitFailed = other.fMaxInitFailed;
255 fMasterResubmitThreshold = other.fMasterResubmitThreshold;
bb885a9e 256 fNtestFiles = other.fNtestFiles;
a3e84053 257 fNrunsPerMaster = other.fNrunsPerMaster;
258 fMaxMergeFiles = other.fMaxMergeFiles;
259 fNsubmitted = other.fNsubmitted;
260 fProductionMode = other.fProductionMode;
cd11251e 261 fOutputToRunNo = other.fOutputToRunNo;
0f389141 262 fMergeViaJDL = other.fMergeViaJDL;
263 fFastReadOption = other.fFastReadOption;
264 fOverwriteMode = other.fOverwriteMode;
c57f56b7 265 fRunNumbers = other.fRunNumbers;
266 fExecutable = other.fExecutable;
0a1c1f7f 267 fExecutableCommand = other.fExecutableCommand;
c57f56b7 268 fArguments = other.fArguments;
631c0b05 269 fExecutableArgs = other.fExecutableArgs;
c57f56b7 270 fAnalysisMacro = other.fAnalysisMacro;
271 fAnalysisSource = other.fAnalysisSource;
d5c6455a 272 fAdditionalRootLibs = other.fAdditionalRootLibs;
c57f56b7 273 fAdditionalLibs = other.fAdditionalLibs;
274 fSplitMode = other.fSplitMode;
275 fAPIVersion = other.fAPIVersion;
276 fROOTVersion = other.fROOTVersion;
277 fAliROOTVersion = other.fAliROOTVersion;
648174cf 278 fExternalPackages = other.fExternalPackages;
c57f56b7 279 fUser = other.fUser;
280 fGridWorkingDir = other.fGridWorkingDir;
281 fGridDataDir = other.fGridDataDir;
282 fDataPattern = other.fDataPattern;
283 fGridOutputDir = other.fGridOutputDir;
284 fOutputArchive = other.fOutputArchive;
285 fOutputFiles = other.fOutputFiles;
286 fInputFormat = other.fInputFormat;
e7c71df0 287 fDatasetName = other.fDatasetName;
c57f56b7 288 fJDLName = other.fJDLName;
bb885a9e 289 fMergeExcludes = other.fMergeExcludes;
f965131e 290 fIncludePath = other.fIncludePath;
bb885a9e 291 fCloseSE = other.fCloseSE;
0df6ccf2 292 fFriendChainName = other.fFriendChainName;
c6cb3634 293 fJobTag = other.fJobTag;
648174cf 294 fOutputSingle = other.fOutputSingle;
5fce53f4 295 fRunPrefix = other.fRunPrefix;
c57f56b7 296 if (other.fInputFiles) {
297 fInputFiles = new TObjArray();
298 TIter next(other.fInputFiles);
299 TObject *obj;
300 while ((obj=next())) fInputFiles->Add(new TObjString(obj->GetName()));
301 fInputFiles->SetOwner();
302 }
4e5c5506 303 if (other.fPackages) {
304 fPackages = new TObjArray();
305 TIter next(other.fPackages);
306 TObject *obj;
307 while ((obj=next())) fPackages->Add(new TObjString(obj->GetName()));
308 fPackages->SetOwner();
309 }
c57f56b7 310 }
311 return *this;
312}
313
f965131e 314//______________________________________________________________________________
315void AliAnalysisAlien::AddIncludePath(const char *path)
316{
317// Add include path in the remote analysis macro.
318 TString p(path);
319 if (p.Contains("-I")) fIncludePath += Form("%s ", path);
320 else fIncludePath += Form("-I%s ", path);
321}
322
c57f56b7 323//______________________________________________________________________________
324void AliAnalysisAlien::AddRunNumber(Int_t run)
325{
326// Add a run number to the list of runs to be processed.
327 if (fRunNumbers.Length()) fRunNumbers += " ";
5fce53f4 328 fRunNumbers += Form("%s%d", fRunPrefix.Data(), run);
c57f56b7 329}
330
ee75cfc3 331//______________________________________________________________________________
332void AliAnalysisAlien::AddRunNumber(const char* run)
333{
334// Add a run number to the list of runs to be processed.
335 if (fRunNumbers.Length()) fRunNumbers += " ";
336 fRunNumbers += run;
337}
338
c57f56b7 339//______________________________________________________________________________
340void AliAnalysisAlien::AddDataFile(const char *lfn)
341{
342// Adds a data file to the input to be analysed. The file should be a valid LFN
343// or point to an existing file in the alien workdir.
344 if (!fInputFiles) fInputFiles = new TObjArray();
345 fInputFiles->Add(new TObjString(lfn));
346}
648174cf 347
348//______________________________________________________________________________
349void AliAnalysisAlien::AddExternalPackage(const char *package)
350{
351// Adds external packages w.r.t to the default ones (root,aliroot and gapi)
352 if (fExternalPackages) fExternalPackages += " ";
353 fExternalPackages += package;
354}
355
c57f56b7 356//______________________________________________________________________________
357Bool_t AliAnalysisAlien::Connect()
358{
359// Try to connect to AliEn. User needs a valid token and /tmp/gclient_env_$UID sourced.
360 if (gGrid && gGrid->IsConnected()) return kTRUE;
361 if (!gSystem->Getenv("alien_API_USER")) {
362 Error("Connect", "Make sure you:\n 1. Have called: alien-token-init <username> today\n 2. Have sourced /tmp/gclient_env_%s",
363 gSystem->Getenv("UID"));
364 return kFALSE;
365 }
366 if (!gGrid) {
367 Info("Connect", "Trying to connect to AliEn ...");
368 TGrid::Connect("alien://");
369 }
370 if (!gGrid || !gGrid->IsConnected()) {
371 Error("Connect", "Did not managed to connect to AliEn. Make sure you have a valid token.");
372 return kFALSE;
373 }
374 fUser = gGrid->GetUser();
375 Info("Connect", "\n##### Connected to AliEn as user %s. Setting analysis user to <%s>", fUser.Data(), fUser.Data());
376 return kTRUE;
377}
378
379//______________________________________________________________________________
380void AliAnalysisAlien::CdWork()
381{
382// Check validity of alien workspace. Create directory if possible.
383 if (!Connect()) {
384 Error("CdWork", "Alien connection required");
385 return;
386 }
387 TString homedir = gGrid->GetHomeDirectory();
388 TString workdir = homedir + fGridWorkingDir;
923e2ca5 389 if (DirectoryExists(workdir)) {
390 gGrid->Cd(workdir);
391 return;
392 }
393 // Work directory not existing - create it
394 gGrid->Cd(homedir);
395 if (gGrid->Mkdir(workdir)) {
396 gGrid->Cd(fGridWorkingDir);
397 Info("CreateJDL", "\n##### Created alien working directory %s", fGridWorkingDir.Data());
398 } else {
399 Warning("CreateJDL", "Working directory %s cannot be created.\n Using %s instead.",
400 workdir.Data(), homedir.Data());
401 fGridWorkingDir = "";
402 }
c57f56b7 403}
404
405//______________________________________________________________________________
406Bool_t AliAnalysisAlien::CheckInputData()
407{
408// Check validity of input data. If necessary, create xml files.
a8739e8a 409 if (!fInputFiles && !fRunNumbers.Length() && !fRunRange[0]) {
d2a409b2 410 if (!fGridDataDir.Length()) {
411 Error("CkeckInputData", "AliEn path to base data directory must be set.\n = Use: SetGridDataDir()");
412 return kFALSE;
413 }
414 Info("CheckInputData", "Analysis will make a single xml for base data directory %s",fGridDataDir.Data());
415 return kTRUE;
c57f56b7 416 }
417 // Process declared files
418 Bool_t is_collection = kFALSE;
419 Bool_t is_xml = kFALSE;
420 Bool_t use_tags = kFALSE;
421 Bool_t checked = kFALSE;
422 CdWork();
423 TString file;
424 TString workdir = gGrid->GetHomeDirectory();
425 workdir += fGridWorkingDir;
426 if (fInputFiles) {
427 TObjString *objstr;
428 TIter next(fInputFiles);
429 while ((objstr=(TObjString*)next())) {
430 file = workdir;
431 file += "/";
432 file += objstr->GetString();
433 // Store full lfn path
434 if (FileExists(file)) objstr->SetString(file);
435 else {
436 file = objstr->GetName();
437 if (!FileExists(objstr->GetName())) {
438 Error("CheckInputData", "Data file %s not found or not in your working dir: %s",
439 objstr->GetName(), workdir.Data());
440 return kFALSE;
441 }
442 }
443 Bool_t iscoll, isxml, usetags;
444 CheckDataType(file, iscoll, isxml, usetags);
445 if (!checked) {
446 checked = kTRUE;
447 is_collection = iscoll;
448 is_xml = isxml;
449 use_tags = usetags;
450 TObject::SetBit(AliAnalysisGrid::kUseTags, use_tags);
451 } else {
452 if ((iscoll != is_collection) || (isxml != is_xml) || (usetags != use_tags)) {
453 Error("CheckInputData", "Some conflict was found in the types of inputs");
454 return kFALSE;
455 }
456 }
457 }
458 }
459 // Process requested run numbers
a8739e8a 460 if (!fRunNumbers.Length() && !fRunRange[0]) return kTRUE;
c57f56b7 461 // Check validity of alien data directory
462 if (!fGridDataDir.Length()) {
463 Error("CkeckInputData", "AliEn path to base data directory must be set.\n = Use: SetGridDataDir()");
464 return kFALSE;
465 }
923e2ca5 466 if (!DirectoryExists(fGridDataDir)) {
c57f56b7 467 Error("CheckInputData", "Data directory %s not existing.", fGridDataDir.Data());
468 return kFALSE;
469 }
470 if (is_collection) {
471 Error("CheckInputData", "You are using raw AliEn collections as input. Cannot process run numbers.");
472 return kFALSE;
473 }
474
475 if (checked && !is_xml) {
476 Error("CheckInputData", "Cannot mix processing of full runs with non-xml files");
477 return kFALSE;
478 }
479 // Check validity of run number(s)
480 TObjArray *arr;
481 TObjString *os;
319593fb 482 Int_t nruns = 0;
904f9f5f 483 TString schunk, schunk2;
c57f56b7 484 TString path;
485 if (!checked) {
486 checked = kTRUE;
487 use_tags = fDataPattern.Contains("tag");
488 TObject::SetBit(AliAnalysisGrid::kUseTags, use_tags);
489 }
490 if (use_tags != fDataPattern.Contains("tag")) {
491 Error("CheckInputData", "Cannot mix input files using/not using tags");
492 return kFALSE;
493 }
494 if (fRunNumbers.Length()) {
a8739e8a 495 Info("CheckDataType", "Using supplied run numbers (run ranges are ignored)");
c57f56b7 496 arr = fRunNumbers.Tokenize(" ");
497 TIter next(arr);
498 while ((os=(TObjString*)next())) {
499 path = Form("%s/%s ", fGridDataDir.Data(), os->GetString().Data());
923e2ca5 500 if (!DirectoryExists(path)) {
501 Warning("CheckInputData", "Run number %s not found in path: <%s>", os->GetString().Data(), path.Data());
a8739e8a 502 continue;
c57f56b7 503 }
504 path = Form("%s/%s.xml", workdir.Data(),os->GetString().Data());
505 TString msg = "\n##### file: ";
506 msg += path;
507 msg += " type: xml_collection;";
508 if (use_tags) msg += " using_tags: Yes";
509 else msg += " using_tags: No";
510 Info("CheckDataType", msg.Data());
319593fb 511 if (fNrunsPerMaster<2) {
d2a409b2 512 AddDataFile(Form("%s.xml", os->GetString().Data()));
319593fb 513 } else {
514 nruns++;
515 if (((nruns-1)%fNrunsPerMaster) == 0) {
516 schunk = os->GetString();
517 }
518 if ((nruns%fNrunsPerMaster)!=0 && os!=arr->Last()) continue;
519 schunk += Form("_%s.xml", os->GetString().Data());
d2a409b2 520 AddDataFile(schunk);
319593fb 521 }
c57f56b7 522 }
523 delete arr;
a8739e8a 524 } else {
525 Info("CheckDataType", "Using run range [%d, %d]", fRunRange[0], fRunRange[1]);
526 for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
5fce53f4 527 path = Form("%s/%s%d ", fGridDataDir.Data(), fRunPrefix.Data(), irun);
923e2ca5 528 if (!DirectoryExists(path)) {
529// Warning("CheckInputData", "Run number %d not found in path: <%s>", irun, path.Data());
a8739e8a 530 continue;
531 }
5fce53f4 532 path = Form("%s/%s%d.xml", workdir.Data(),fRunPrefix.Data(),irun);
a8739e8a 533 TString msg = "\n##### file: ";
534 msg += path;
535 msg += " type: xml_collection;";
536 if (use_tags) msg += " using_tags: Yes";
537 else msg += " using_tags: No";
538 Info("CheckDataType", msg.Data());
319593fb 539 if (fNrunsPerMaster<2) {
5fce53f4 540 AddDataFile(Form("%s%d.xml",fRunPrefix.Data(),irun));
319593fb 541 } else {
542 nruns++;
543 if (((nruns-1)%fNrunsPerMaster) == 0) {
5fce53f4 544 schunk = Form("%s%d", fRunPrefix.Data(),irun);
319593fb 545 }
904f9f5f 546 schunk2 = Form("_%s%d.xml", fRunPrefix.Data(), irun);
319593fb 547 if ((nruns%fNrunsPerMaster)!=0 && irun != fRunRange[1]) continue;
904f9f5f 548 schunk += schunk2;
d2a409b2 549 AddDataFile(schunk);
319593fb 550 }
a8739e8a 551 }
904f9f5f 552 if (!fInputFiles) {
553 schunk += schunk2;
554 AddDataFile(schunk);
555 }
c57f56b7 556 }
557 return kTRUE;
558}
559
560//______________________________________________________________________________
561Bool_t AliAnalysisAlien::CreateDataset(const char *pattern)
562{
563// Create dataset for the grid data directory + run number.
564 if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE;
565 if (!Connect()) {
566 Error("CreateDataset", "Cannot create dataset with no grid connection");
567 return kFALSE;
568 }
569
570 // Cd workspace
571 CdWork();
572 TString workdir = gGrid->GetHomeDirectory();
573 workdir += fGridWorkingDir;
574
575 // Compose the 'find' command arguments
576 TString command;
577 TString options = "-x collection ";
bb885a9e 578 if (TestBit(AliAnalysisGrid::kTest)) options += Form("-l %d ", fNtestFiles);
c57f56b7 579 TString conditions = "";
580
581 TString file;
582 TString path;
319593fb 583 Int_t nruns = 0;
904f9f5f 584 TString schunk, schunk2;
ab254fd1 585 TGridCollection *cbase=0, *cadd=0;
d2a409b2 586 if (!fRunNumbers.Length() && !fRunRange[0]) {
587 if (fInputFiles && fInputFiles->GetEntries()) return kTRUE;
588 // Make a single data collection from data directory.
589 path = fGridDataDir;
923e2ca5 590 if (!DirectoryExists(path)) {
d2a409b2 591 Error("CreateDataset", "Path to data directory %s not valid",fGridDataDir.Data());
592 return kFALSE;
593 }
923e2ca5 594// CdWork();
d2a409b2 595 if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
596 else file = Form("%s.xml", gSystem->BaseName(path));
0f389141 597 if (gSystem->AccessPathName(file) || TestBit(AliAnalysisGrid::kTest) || fOverwriteMode) {
d2a409b2 598 command = "find ";
599 command += options;
600 command += path;
601 command += " ";
602 command += pattern;
603 command += conditions;
84fcd93f 604 printf("command: %s\n", command.Data());
d2a409b2 605 TGridResult *res = gGrid->Command(command);
606 if (res) delete res;
607 // Write standard output to file
608 gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", file.Data()));
0f389141 609 }
610 Bool_t fileExists = FileExists(file);
611 if (!TestBit(AliAnalysisGrid::kTest) && (!fileExists || fOverwriteMode)) {
d2a409b2 612 // Copy xml file to alien space
0f389141 613 if (fileExists) gGrid->Rm(file);
d2a409b2 614 TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
615 if (!FileExists(file)) {
616 Error("CreateDataset", "Command %s did NOT succeed", command.Data());
617 return kFALSE;
618 }
619 // Update list of files to be processed.
620 }
621 AddDataFile(Form("%s/%s", workdir.Data(), file.Data()));
622 return kTRUE;
623 }
c57f56b7 624 // Several runs
a8739e8a 625 if (fRunNumbers.Length()) {
626 TObjArray *arr = fRunNumbers.Tokenize(" ");
627 TObjString *os;
628 TIter next(arr);
629 while ((os=(TObjString*)next())) {
630 path = Form("%s/%s ", fGridDataDir.Data(), os->GetString().Data());
923e2ca5 631 if (!DirectoryExists(path)) continue;
632// CdWork();
a8739e8a 633 if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
634 else file = Form("%s.xml", os->GetString().Data());
319593fb 635 // If local collection file does not exist, create it via 'find' command.
636 if (gSystem->AccessPathName(file)) {
637 command = "find ";
638 command += options;
639 command += path;
640 command += pattern;
641 command += conditions;
642 TGridResult *res = gGrid->Command(command);
643 if (res) delete res;
644 // Write standard output to file
645 gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", file.Data()));
646 }
a8739e8a 647 if (TestBit(AliAnalysisGrid::kTest)) break;
319593fb 648 // Check if there is one run per master job.
649 if (fNrunsPerMaster<2) {
650 if (FileExists(file)) {
0f389141 651 if (fOverwriteMode) gGrid->Rm(file);
652 else {
653 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
654 continue;
655 }
319593fb 656 }
657 // Copy xml file to alien space
658 TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
659 if (!FileExists(file)) {
660 Error("CreateDataset", "Command %s did NOT succeed", command.Data());
661 delete arr;
662 return kFALSE;
663 }
664 } else {
665 nruns++;
666 if (((nruns-1)%fNrunsPerMaster) == 0) {
667 schunk = os->GetString();
668 cbase = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
669 } else {
670 cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
84fcd93f 671 printf(" Merging collection <%s> into masterjob input...\n", file.Data());
319593fb 672 cbase->Add(cadd);
673 delete cadd;
674 }
675 if ((nruns%fNrunsPerMaster)!=0 && os!=arr->Last()) {
676 continue;
677 }
678 schunk += Form("_%s.xml", os->GetString().Data());
0f389141 679 if (FileExists(schunk)) {
680 if (fOverwriteMode) gGrid->Rm(file);
681 else {
682 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data());
683 continue;
684 }
319593fb 685 }
84fcd93f 686 printf("Exporting merged collection <%s> and copying to AliEn\n", schunk.Data());
319593fb 687 cbase->ExportXML(Form("file://%s", schunk.Data()),kFALSE,kFALSE, schunk, "Merged runs");
e95434bc 688 TFile::Cp(Form("file:%s",schunk.Data()), Form("alien://%s/%s",workdir.Data(), schunk.Data()));
319593fb 689 if (!FileExists(schunk)) {
690 Error("CreateDataset", "Copy command did NOT succeed for %s", schunk.Data());
691 delete arr;
692 return kFALSE;
693 }
694 }
a8739e8a 695 }
696 delete arr;
697 } else {
698 // Process a full run range.
699 for (Int_t irun=fRunRange[0]; irun<=fRunRange[1]; irun++) {
5fce53f4 700 path = Form("%s/%s%d ", fGridDataDir.Data(), fRunPrefix.Data(), irun);
923e2ca5 701 if (!DirectoryExists(path)) continue;
702// CdWork();
a8739e8a 703 if (TestBit(AliAnalysisGrid::kTest)) file = "wn.xml";
5fce53f4 704 else file = Form("%s%d.xml", fRunPrefix.Data(), irun);
0f389141 705 if (FileExists(file) && fNrunsPerMaster<2 && !TestBit(AliAnalysisGrid::kTest)) {
706 if (fOverwriteMode) gGrid->Rm(file);
707 else {
708 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
709 continue;
710 }
a8739e8a 711 }
319593fb 712 // If local collection file does not exist, create it via 'find' command.
0f389141 713 if (gSystem->AccessPathName(file) || fOverwriteMode) {
319593fb 714 command = "find ";
715 command += options;
716 command += path;
717 command += pattern;
718 command += conditions;
719 TGridResult *res = gGrid->Command(command);
720 if (res) delete res;
721 // Write standard output to file
722 gROOT->ProcessLine(Form("gGrid->Stdout(); > %s", file.Data()));
723 }
a8739e8a 724 if (TestBit(AliAnalysisGrid::kTest)) break;
319593fb 725 // Check if there is one run per master job.
726 if (fNrunsPerMaster<2) {
727 if (FileExists(file)) {
0f389141 728 if (fOverwriteMode) gGrid->Rm(file);
729 else {
730 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", file.Data());
731 continue;
732 }
319593fb 733 }
734 // Copy xml file to alien space
735 TFile::Cp(Form("file:%s",file.Data()), Form("alien://%s/%s",workdir.Data(), file.Data()));
736 if (!FileExists(file)) {
737 Error("CreateDataset", "Command %s did NOT succeed", command.Data());
738 return kFALSE;
739 }
740 } else {
741 nruns++;
95e5b448 742 // Check if the collection for the chunk exist locally.
743 Int_t nchunk = (nruns-1)/fNrunsPerMaster;
0f389141 744 if (FileExists(fInputFiles->At(nchunk)->GetName())) {
745 if (fOverwriteMode) gGrid->Rm(fInputFiles->At(nchunk)->GetName());
746 else continue;
747 }
84fcd93f 748 printf(" Merging collection <%s> into %d runs chunk...\n",file.Data(),fNrunsPerMaster);
319593fb 749 if (((nruns-1)%fNrunsPerMaster) == 0) {
904f9f5f 750 schunk = Form("%s%d", fRunPrefix.Data(), irun);
319593fb 751 cbase = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
752 } else {
753 cadd = (TGridCollection*)gROOT->ProcessLine(Form("new TAlienCollection(\"%s\", 1000000);",file.Data()));
754 cbase->Add(cadd);
755 delete cadd;
756 }
904f9f5f 757 schunk2 = Form("%s_%s%d.xml", schunk.Data(), fRunPrefix.Data(), irun);
758 if ((nruns%fNrunsPerMaster)!=0 && irun!=fRunRange[1] && schunk2 != fInputFiles->Last()->GetName()) {
319593fb 759 continue;
760 }
904f9f5f 761 schunk = schunk2;
319593fb 762 if (FileExists(schunk)) {
0f389141 763 if (fOverwriteMode) gGrid->Rm(schunk);
764 else {
765 Info("CreateDataset", "\n##### Dataset %s exist. Skipping creation...", schunk.Data());
766 continue;
767 }
319593fb 768 }
84fcd93f 769 printf("Exporting merged collection <%s> and copying to AliEn.\n", schunk.Data());
319593fb 770 cbase->ExportXML(Form("file://%s", schunk.Data()),kFALSE,kFALSE, schunk, "Merged runs");
95e5b448 771 if (FileExists(schunk)) {
0f389141 772 if (fOverwriteMode) gGrid->Rm(schunk);
773 else {
774 Info("CreateDataset", "\n##### Dataset %s exist. Skipping copy...", schunk.Data());
775 continue;
776 }
95e5b448 777 }
319593fb 778 TFile::Cp(Form("file:%s",schunk.Data()), Form("alien://%s/%s",workdir.Data(), schunk.Data()));
779 if (!FileExists(schunk)) {
780 Error("CreateDataset", "Copy command did NOT succeed for %s", schunk.Data());
781 return kFALSE;
782 }
783 }
c57f56b7 784 }
a8739e8a 785 }
c57f56b7 786 return kTRUE;
787}
788
789//______________________________________________________________________________
790Bool_t AliAnalysisAlien::CreateJDL()
791{
792// Generate a JDL file according to current settings. The name of the file is
793// specified by fJDLName.
794 Bool_t error = kFALSE;
795 TObjArray *arr = 0;
796 Bool_t copy = kTRUE;
797 if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
798 Bool_t generate = kTRUE;
799 if (TestBit(AliAnalysisGrid::kTest) || TestBit(AliAnalysisGrid::kSubmit)) generate = kFALSE;
800 if (!Connect()) {
801 Error("CreateJDL", "Alien connection required");
802 return kFALSE;
803 }
804 // Check validity of alien workspace
805 CdWork();
806 TString workdir = gGrid->GetHomeDirectory();
807 workdir += fGridWorkingDir;
808 if (generate) {
809 TObjString *os;
810 if (!fInputFiles) {
811 Error("CreateJDL()", "Define some input files for your analysis.");
812 error = kTRUE;
813 }
814 // Compose list of input files
815 // Check if output files were defined
816 if (!fOutputFiles.Length()) {
817 Error("CreateJDL", "You must define at least one output file");
818 error = kTRUE;
819 }
820 // Check if an output directory was defined and valid
821 if (!fGridOutputDir.Length()) {
822 Error("CreateJDL", "You must define AliEn output directory");
823 error = kTRUE;
824 } else {
d2a409b2 825 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
923e2ca5 826 if (!DirectoryExists(fGridOutputDir)) {
c57f56b7 827 if (gGrid->Mkdir(fGridOutputDir)) {
828 Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
829 } else {
830 Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
5513444a 831 // error = kTRUE;
c57f56b7 832 }
833 }
834 gGrid->Cd(workdir);
835 }
836 // Exit if any error up to now
837 if (error) return kFALSE;
838 // Set JDL fields
0f389141 839 if (!fUser.IsNull()) {
840 fGridJDL->SetValue("User", Form("\"%s\"", fUser.Data()));
841 fMergingJDL->SetValue("User", Form("\"%s\"", fUser.Data()));
842 }
843 fGridJDL->SetExecutable(fExecutable, "This is the startup script");
844 TString mergeExec = fExecutable;
845 mergeExec.ReplaceAll(".sh", "_merge.sh");
846 fMergingJDL->SetExecutable(mergeExec, "This is the startup script");
847 mergeExec.ReplaceAll(".sh", ".C");
848 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),mergeExec.Data()), "List of input files to be uploaded to workers");
b5b9dee8 849 if (!fArguments.IsNull())
850 fGridJDL->SetArguments(fArguments, "Arguments for the executable command");
1f0d1ca2 851 fMergingJDL->SetArguments("$1");
852 fGridJDL->SetValue("TTL", Form("\"%d\"",fTTL));
853 fGridJDL->SetDescription("TTL", Form("Time after which the job is killed (%d min.)", fTTL/60));
854 fMergingJDL->SetValue("TTL", Form("\"%d\"",fTTL));
855 fMergingJDL->SetDescription("TTL", Form("Time after which the job is killed (%d min.)", fTTL/60));
856
0f389141 857 if (fMaxInitFailed > 0) {
c57f56b7 858 fGridJDL->SetValue("MaxInitFailed", Form("\"%d\"",fMaxInitFailed));
0f389141 859 fGridJDL->SetDescription("MaxInitFailed", "Maximum number of first failing jobs to abort the master job");
860 }
861 if (fSplitMaxInputFileNumber > 0) {
c57f56b7 862 fGridJDL->SetValue("SplitMaxInputFileNumber", Form("\"%d\"", fSplitMaxInputFileNumber));
0f389141 863 fGridJDL->SetDescription("SplitMaxInputFileNumber", "Maximum number of input files to be processed per subjob");
864 }
865 if (fSplitMode.Length()) {
c57f56b7 866 fGridJDL->SetValue("Split", Form("\"%s\"", fSplitMode.Data()));
0f389141 867 fGridJDL->SetDescription("Split", "We split per SE or file");
868 }
869 if (!fAliROOTVersion.IsNull()) {
870 fGridJDL->AddToPackages("AliRoot", fAliROOTVersion,"VO_ALICE", "List of requested packages");
871 fMergingJDL->AddToPackages("AliRoot", fAliROOTVersion, "VO_ALICE", "List of requested packages");
872 }
873 if (!fROOTVersion.IsNull()) {
c57f56b7 874 fGridJDL->AddToPackages("ROOT", fROOTVersion);
0f389141 875 fMergingJDL->AddToPackages("ROOT", fROOTVersion);
876 }
877 if (!fAPIVersion.IsNull()) {
c57f56b7 878 fGridJDL->AddToPackages("APISCONFIG", fAPIVersion);
0f389141 879 fMergingJDL->AddToPackages("APISCONFIG", fAPIVersion);
880 }
648174cf 881 if (!fExternalPackages.IsNull()) {
882 arr = fExternalPackages.Tokenize(" ");
883 TIter next(arr);
884 while ((os=(TObjString*)next())) {
885 TString pkgname = os->GetString();
886 Int_t index = pkgname.Index("::");
887 TString pkgversion = pkgname(index+2, pkgname.Length());
888 pkgname.Remove(index);
889 fGridJDL->AddToPackages(pkgname, pkgversion);
0f389141 890 fMergingJDL->AddToPackages(pkgname, pkgversion);
648174cf 891 }
892 delete arr;
893 }
0f389141 894 fGridJDL->SetInputDataListFormat(fInputFormat, "Format of input data");
895 fGridJDL->SetInputDataList("wn.xml", "Collection name to be processed on each worker node");
896 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), fAnalysisMacro.Data()), "List of input files to be uploaded to workers");
f10e8481 897 TString analysisFile = fExecutable;
898 analysisFile.ReplaceAll(".sh", ".root");
899 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),analysisFile.Data()));
f866cba5 900 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(),analysisFile.Data()));
c57f56b7 901 if (IsUsingTags() && !gSystem->AccessPathName("ConfigureCuts.C"))
902 fGridJDL->AddToInputSandbox(Form("LF:%s/ConfigureCuts.C", workdir.Data()));
903 if (fAdditionalLibs.Length()) {
904 arr = fAdditionalLibs.Tokenize(" ");
905 TIter next(arr);
906 while ((os=(TObjString*)next())) {
907 if (os->GetString().Contains(".so")) continue;
908 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), os->GetString().Data()));
0f389141 909 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), os->GetString().Data()));
c57f56b7 910 }
911 delete arr;
912 }
4e5c5506 913 if (fPackages) {
914 TIter next(fPackages);
915 TObject *obj;
0f389141 916 while ((obj=next())) {
4e5c5506 917 fGridJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), obj->GetName()));
0f389141 918 fMergingJDL->AddToInputSandbox(Form("LF:%s/%s", workdir.Data(), obj->GetName()));
919 }
4e5c5506 920 }
c57f56b7 921 if (fOutputArchive.Length()) {
922 arr = fOutputArchive.Tokenize(" ");
923 TIter next(arr);
0f389141 924 Bool_t first = kTRUE;
925 const char *comment = "Files to be archived";
926 const char *comment1 = comment;
927 while ((os=(TObjString*)next())) {
928 if (!first) comment = NULL;
929 if (!os->GetString().Contains("@") && fCloseSE.Length())
930 fGridJDL->AddToOutputArchive(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
931 else
932 fGridJDL->AddToOutputArchive(os->GetString(), comment);
933 first = kFALSE;
934 }
c57f56b7 935 delete arr;
0f389141 936 TString outputArchive = fOutputArchive;
937 if (!fMergeExcludes.IsNull()) {
938 arr = fMergeExcludes.Tokenize(" ");
705adb3e 939 TIter next1(arr);
940 while ((os=(TObjString*)next1())) {
0f389141 941 outputArchive.ReplaceAll(Form("%s,",os->GetString().Data()),"");
942 outputArchive.ReplaceAll(os->GetString(),"");
943 }
944 delete arr;
945 }
946 arr = outputArchive.Tokenize(" ");
705adb3e 947 TIter next2(arr);
0f389141 948 comment = comment1;
949 first = kTRUE;
705adb3e 950 while ((os=(TObjString*)next2())) {
0f389141 951 if (!first) comment = NULL;
952 if (!os->GetString().Contains("@") && fCloseSE.Length())
953 fMergingJDL->AddToOutputArchive(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
954 else
955 fMergingJDL->AddToOutputArchive(os->GetString(), comment);
956 first = kFALSE;
957 }
958 delete arr;
c57f56b7 959 }
c57f56b7 960 arr = fOutputFiles.Tokenize(" ");
961 TIter next(arr);
0f389141 962 Bool_t first = kTRUE;
963 const char *comment = "Files to be archived";
964 const char *comment1 = comment;
43da816a 965 while ((os=(TObjString*)next())) {
e1eaf596 966 // Ignore ouputs in jdl that are also in outputarchive
967 TString sout = os->GetString();
968 if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
969 if (fOutputArchive.Contains(sout)) continue;
0f389141 970 if (!first) comment = NULL;
43da816a 971 if (!os->GetString().Contains("@") && fCloseSE.Length())
0f389141 972 fGridJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
43da816a 973 else
0f389141 974 fGridJDL->AddToOutputSandbox(os->GetString(), comment);
975 first = kFALSE;
43da816a 976 }
c57f56b7 977 delete arr;
0f389141 978 if (fOutputFiles.Length()) {
979 TString outputFiles = fOutputFiles;
980 if (!fMergeExcludes.IsNull()) {
981 arr = fMergeExcludes.Tokenize(" ");
705adb3e 982 TIter next1(arr);
983 while ((os=(TObjString*)next1())) {
0f389141 984 outputFiles.ReplaceAll(Form("%s,",os->GetString().Data()),"");
985 outputFiles.ReplaceAll(os->GetString(),"");
986 }
987 delete arr;
988 }
989 arr = outputFiles.Tokenize(" ");
705adb3e 990 TIter next2(arr);
0f389141 991 comment = comment1;
992 first = kTRUE;
705adb3e 993 while ((os=(TObjString*)next2())) {
0f389141 994 // Ignore ouputs in jdl that are also in outputarchive
995 TString sout = os->GetString();
996 if (sout.Index("@")>0) sout.Remove(sout.Index("@"));
997 if (fOutputArchive.Contains(sout)) continue;
998 if (!first) comment = NULL;
999 if (!os->GetString().Contains("@") && fCloseSE.Length())
1000 fMergingJDL->AddToOutputSandbox(Form("%s@%s",os->GetString().Data(), fCloseSE.Data()), comment);
1001 else
1002 fMergingJDL->AddToOutputSandbox(os->GetString(), comment);
1003 }
1004 delete arr;
1005 }
1006 fGridJDL->SetPrice((UInt_t)fPrice, "AliEn price for this job");
1007 fMergingJDL->SetPrice((UInt_t)fPrice, "AliEn price for this job");
0d5d317c 1008 TString validationScript = fExecutable;
1009 validationScript.ReplaceAll(".sh", "_validation.sh");
0f389141 1010 fGridJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()), "Validation script to be run for each subjob");
1011 validationScript = fExecutable;
1012 validationScript.ReplaceAll(".sh", "_mergevalidation.sh");
1013 fMergingJDL->SetValidationCommand(Form("%s/%s", workdir.Data(),validationScript.Data()), "Validation script to be run for each subjob");
1014 if (fMasterResubmitThreshold) {
1015 fGridJDL->SetValue("MasterResubmitThreshold", Form("\"%d%%\"", fMasterResubmitThreshold));
1016 fGridJDL->SetDescription("MasterResubmitThreshold", "Resubmit failed jobs until DONE rate reaches this percentage");
1017 }
d2a409b2 1018 // Write a jdl with 2 input parameters: collection name and output dir name.
1019 WriteJDL(copy);
c57f56b7 1020 }
1021 // Copy jdl to grid workspace
a8739e8a 1022 if (copy) {
b5e4aaa7 1023 // Check if an output directory was defined and valid
1024 if (!fGridOutputDir.Length()) {
1025 Error("CreateJDL", "You must define AliEn output directory");
1026 return kFALSE;
1027 } else {
1028 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("%s/%s", workdir.Data(), fGridOutputDir.Data());
bb2e67a0 1029 if (!fProductionMode && !DirectoryExists(fGridOutputDir)) {
b5e4aaa7 1030 if (gGrid->Mkdir(fGridOutputDir)) {
1031 Info("CreateJDL", "\n##### Created alien output directory %s", fGridOutputDir.Data());
1032 } else {
1033 Error("CreateJDL", "Could not create alien output directory %s", fGridOutputDir.Data());
1034 return kFALSE;
1035 }
1036 }
1037 gGrid->Cd(workdir);
1038 }
648174cf 1039 if (TestBit(AliAnalysisGrid::kSubmit)) {
0f389141 1040 TString mergeJDLName = fExecutable;
1041 mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
648174cf 1042 TString locjdl = Form("%s/%s", fGridOutputDir.Data(),fJDLName.Data());
0f389141 1043 TString locjdl1 = Form("%s/%s", fGridOutputDir.Data(),mergeJDLName.Data());
1044 if (fProductionMode) {
648174cf 1045 locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
0f389141 1046 locjdl1 = Form("%s/%s", workdir.Data(),mergeJDLName.Data());
1047 }
648174cf 1048 if (FileExists(locjdl)) gGrid->Rm(locjdl);
0f389141 1049 if (FileExists(locjdl1)) gGrid->Rm(locjdl1);
1050 Info("CreateJDL", "\n##### Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
648174cf 1051 TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s", locjdl.Data()));
0f389141 1052 if (fMergeViaJDL) {
1053 Info("CreateJDL", "\n##### Copying merging JDL file <%s> to your AliEn output directory", mergeJDLName.Data());
1054 TFile::Cp(Form("file:%s",mergeJDLName.Data()), Form("alien://%s", locjdl1.Data()));
1055 }
648174cf 1056 }
c57f56b7 1057 if (fAdditionalLibs.Length()) {
e7c71df0 1058 arr = fAdditionalLibs.Tokenize(" ");
c57f56b7 1059 TObjString *os;
1060 TIter next(arr);
1061 while ((os=(TObjString*)next())) {
c57f56b7 1062 if (os->GetString().Contains(".so")) continue;
4e5c5506 1063 Info("CreateJDL", "\n##### Copying dependency: <%s> to your alien workspace", os->GetString().Data());
c57f56b7 1064 if (FileExists(os->GetString())) gGrid->Rm(os->GetString());
1065 TFile::Cp(Form("file:%s",os->GetString().Data()), Form("alien://%s/%s", workdir.Data(), os->GetString().Data()));
1066 }
1067 delete arr;
1068 }
4e5c5506 1069 if (fPackages) {
1070 TIter next(fPackages);
1071 TObject *obj;
1072 while ((obj=next())) {
fdbbc7be 1073 if (FileExists(obj->GetName())) gGrid->Rm(obj->GetName());
4e5c5506 1074 Info("CreateJDL", "\n##### Copying dependency: <%s> to your alien workspace", obj->GetName());
1075 TFile::Cp(Form("file:%s",obj->GetName()), Form("alien://%s/%s", workdir.Data(), obj->GetName()));
1076 }
1077 }
c57f56b7 1078 }
1079 return kTRUE;
1080}
1081
a8739e8a 1082//______________________________________________________________________________
d2a409b2 1083Bool_t AliAnalysisAlien::WriteJDL(Bool_t copy)
a8739e8a 1084{
1085// Writes one or more JDL's corresponding to findex. If findex is negative,
1086// all run numbers are considered in one go (jdl). For non-negative indices
1087// they correspond to the indices in the array fInputFiles.
1088 if (!fInputFiles) return kFALSE;
1089 TObjString *os;
a8739e8a 1090 TString workdir = gGrid->GetHomeDirectory();
1091 workdir += fGridWorkingDir;
d2a409b2 1092
1093 if (!fRunNumbers.Length() && !fRunRange[0]) {
1094 // One jdl with no parameters in case input data is specified by name.
a8739e8a 1095 TIter next(fInputFiles);
1096 while ((os=(TObjString*)next()))
0f389141 1097 fGridJDL->AddToInputDataCollection(Form("LF:%s,nodownload", os->GetString().Data()), "Input xml collections");
648174cf 1098 if (!fOutputSingle.IsNull())
0f389141 1099 fGridJDL->SetOutputDirectory(Form("#alienfulldir#/../%s",fOutputSingle.Data()), "Output directory");
1100 else {
1101 fGridJDL->SetOutputDirectory(Form("%s/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
1102 fMergingJDL->SetOutputDirectory(fGridOutputDir);
1103 }
a8739e8a 1104 } else {
d2a409b2 1105 // One jdl to be submitted with 2 input parameters: data collection name and output dir prefix
0f389141 1106 fGridJDL->AddToInputDataCollection(Form("LF:%s/$1,nodownload", workdir.Data()), "Input xml collections");
cd11251e 1107 if (!fOutputSingle.IsNull()) {
0f389141 1108 if (!fOutputToRunNo) fGridJDL->SetOutputDirectory(Form("#alienfulldir#/%s",fOutputSingle.Data()), "Output directory");
1109 else fGridJDL->SetOutputDirectory(Form("%s/$2",fGridOutputDir.Data()), "Output directory");
cd11251e 1110 } else {
0f389141 1111 fGridJDL->SetOutputDirectory(Form("%s/$2/#alien_counter_03i#", fGridOutputDir.Data()), "Output directory");
1112 fMergingJDL->SetOutputDirectory(Form("%s/$1", fGridOutputDir.Data()), "Output directory");
cd11251e 1113 }
a8739e8a 1114 }
1115
1116
1117 // Generate the JDL as a string
1118 TString sjdl = fGridJDL->Generate();
0f389141 1119 TString sjdl1 = fMergingJDL->Generate();
a8739e8a 1120 Int_t index;
a8739e8a 1121 sjdl.ReplaceAll("\"LF:", "\n \"LF:");
1122 sjdl.ReplaceAll("(member", "\n (member");
1123 sjdl.ReplaceAll("\",\"VO_", "\",\n \"VO_");
1124 sjdl.ReplaceAll("{", "{\n ");
1125 sjdl.ReplaceAll("};", "\n};");
1126 sjdl.ReplaceAll("{\n \n", "{\n");
1127 sjdl.ReplaceAll("\n\n", "\n");
1128 sjdl.ReplaceAll("OutputDirectory", "OutputDir");
0f389141 1129 sjdl1.ReplaceAll("\"LF:", "\n \"LF:");
1130 sjdl1.ReplaceAll("(member", "\n (member");
1131 sjdl1.ReplaceAll("\",\"VO_", "\",\n \"VO_");
1132 sjdl1.ReplaceAll("{", "{\n ");
1133 sjdl1.ReplaceAll("};", "\n};");
1134 sjdl1.ReplaceAll("{\n \n", "{\n");
1135 sjdl1.ReplaceAll("\n\n", "\n");
1136 sjdl1.ReplaceAll("OutputDirectory", "OutputDir");
a8739e8a 1137 sjdl += "JDLVariables = \n{\n \"Packages\",\n \"OutputDir\"\n};\n";
f60ef0ba 1138 sjdl.Prepend(Form("Jobtag = {\n \"comment:%s\"\n};\n", fJobTag.Data()));
a8739e8a 1139 index = sjdl.Index("JDLVariables");
1140 if (index >= 0) sjdl.Insert(index, "\n# JDL variables\n");
0f389141 1141 sjdl1 += "JDLVariables = \n{\n \"Packages\",\n \"OutputDir\"\n};\n";
1142 sjdl1.Prepend(Form("Jobtag = {\n \"comment:Merging_%s\"\n};\n", fJobTag.Data()));
1143 index = sjdl1.Index("JDLVariables");
1144 if (index >= 0) sjdl1.Insert(index, "\n# JDL variables\n");
a8739e8a 1145 // Write jdl to file
a8739e8a 1146 ofstream out;
d2a409b2 1147 out.open(fJDLName.Data(), ios::out);
a8739e8a 1148 if (out.bad()) {
d2a409b2 1149 Error("CreateJDL", "Bad file name: %s", fJDLName.Data());
a8739e8a 1150 return kFALSE;
1151 }
1152 out << sjdl << endl;
0f389141 1153 TString mergeJDLName = fExecutable;
1154 mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
1155 if (fMergeViaJDL) {
1156 ofstream out1;
1157 out1.open(mergeJDLName.Data(), ios::out);
1158 if (out.bad()) {
1159 Error("CreateJDL", "Bad file name: %s", mergeJDLName.Data());
1160 return kFALSE;
1161 }
1162 out1 << sjdl1 << endl;
1163 }
a8739e8a 1164
1165 // Copy jdl to grid workspace
1166 if (!copy) {
1167 Info("CreateJDL", "\n##### You may want to review jdl:%s and analysis macro:%s before running in <submit> mode", fJDLName.Data(), fAnalysisMacro.Data());
1168 } else {
d2a409b2 1169 TString locjdl = Form("%s/%s", fGridOutputDir.Data(),fJDLName.Data());
0f389141 1170 TString locjdl1 = Form("%s/%s", fGridOutputDir.Data(),mergeJDLName.Data());
1171 if (fProductionMode) {
b5fe9cba 1172 locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
0f389141 1173 locjdl1 = Form("%s/%s", workdir.Data(),mergeJDLName.Data());
1174 }
d2a409b2 1175 if (FileExists(locjdl)) gGrid->Rm(locjdl);
0f389141 1176 if (FileExists(locjdl1)) gGrid->Rm(locjdl1);
1177 Info("CreateJDL", "\n##### Copying JDL file <%s> to your AliEn output directory", fJDLName.Data());
5513444a 1178 TFile::Cp(Form("file:%s",fJDLName.Data()), Form("alien://%s", locjdl.Data()));
0f389141 1179 if (fMergeViaJDL) {
1180 Info("CreateJDL", "\n##### Copying merging JDL file <%s> to your AliEn output directory", mergeJDLName.Data());
1181 TFile::Cp(Form("file:%s",mergeJDLName.Data()), Form("alien://%s", locjdl1.Data()));
1182 }
a8739e8a 1183 }
1184 return kTRUE;
1185}
1186
c57f56b7 1187//______________________________________________________________________________
5513444a 1188Bool_t AliAnalysisAlien::FileExists(const char *lfn)
c57f56b7 1189{
1190// Returns true if file exists.
5513444a 1191 if (!gGrid) return kFALSE;
c57f56b7 1192 TGridResult *res = gGrid->Ls(lfn);
1193 if (!res) return kFALSE;
1194 TMap *map = dynamic_cast<TMap*>(res->At(0));
1195 if (!map) {
1196 delete res;
1197 return kFALSE;
1198 }
1199 TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("name"));
1200 if (!objs || !objs->GetString().Length()) {
1201 delete res;
1202 return kFALSE;
1203 }
1204 delete res;
1205 return kTRUE;
1206}
1207
923e2ca5 1208//______________________________________________________________________________
1209Bool_t AliAnalysisAlien::DirectoryExists(const char *dirname)
1210{
1211// Returns true if directory exists. Can be also a path.
1212 if (!gGrid) return kFALSE;
1213 // Check if dirname is a path
1214 TString dirstripped = dirname;
1215 dirstripped = dirstripped.Strip();
1216 dirstripped = dirstripped.Strip(TString::kTrailing, '/');
1217 TString dir = gSystem->BaseName(dirstripped);
1218 dir += "/";
1219 TString path = gSystem->DirName(dirstripped);
1220 TGridResult *res = gGrid->Ls(path, "-F");
1221 if (!res) return kFALSE;
1222 TIter next(res);
1223 TMap *map;
1224 TObject *obj;
1225 while ((map=dynamic_cast<TMap*>(next()))) {
1226 obj = map->GetValue("name");
1227 if (!obj) break;
1228 if (dir == obj->GetName()) {
1229 delete res;
1230 return kTRUE;
1231 }
1232 }
1233 delete res;
1234 return kFALSE;
1235}
1236
c57f56b7 1237//______________________________________________________________________________
1238void AliAnalysisAlien::CheckDataType(const char *lfn, Bool_t &is_collection, Bool_t &is_xml, Bool_t &use_tags)
1239{
1240// Check input data type.
1241 is_collection = kFALSE;
1242 is_xml = kFALSE;
1243 use_tags = kFALSE;
1244 if (!gGrid) {
1245 Error("CheckDataType", "No connection to grid");
1246 return;
1247 }
1248 is_collection = IsCollection(lfn);
1249 TString msg = "\n##### file: ";
1250 msg += lfn;
1251 if (is_collection) {
1252 msg += " type: raw_collection;";
1253 // special treatment for collections
1254 is_xml = kFALSE;
1255 // check for tag files in the collection
1256 TGridResult *res = gGrid->Command(Form("listFilesFromCollection -z -v %s",lfn), kFALSE);
1257 if (!res) {
1258 msg += " using_tags: No (unknown)";
1259 Info("CheckDataType", msg.Data());
1260 return;
1261 }
1262 const char* typeStr = res->GetKey(0, "origLFN");
1263 if (!typeStr || !strlen(typeStr)) {
1264 msg += " using_tags: No (unknown)";
1265 Info("CheckDataType", msg.Data());
1266 return;
1267 }
1268 TString file = typeStr;
1269 use_tags = file.Contains(".tag");
1270 if (use_tags) msg += " using_tags: Yes";
1271 else msg += " using_tags: No";
1272 Info("CheckDataType", msg.Data());
1273 return;
1274 }
1275 TString slfn(lfn);
1276 slfn.ToLower();
1277 is_xml = slfn.Contains(".xml");
1278 if (is_xml) {
1279 // Open xml collection and check if there are tag files inside
1280 msg += " type: xml_collection;";
1281 TGridCollection *coll = (TGridCollection*)gROOT->ProcessLine(Form("TAlienCollection::Open(\"alien://%s\",1);",lfn));
1282 if (!coll) {
1283 msg += " using_tags: No (unknown)";
1284 Info("CheckDataType", msg.Data());
1285 return;
1286 }
1287 TMap *map = coll->Next();
1288 if (!map) {
1289 msg += " using_tags: No (unknown)";
1290 Info("CheckDataType", msg.Data());
1291 return;
1292 }
1293 map = (TMap*)map->GetValue("");
1294 TString file;
1295 if (map && map->GetValue("name")) file = map->GetValue("name")->GetName();
1296 use_tags = file.Contains(".tag");
1297 delete coll;
1298 if (use_tags) msg += " using_tags: Yes";
1299 else msg += " using_tags: No";
1300 Info("CheckDataType", msg.Data());
1301 return;
1302 }
1303 use_tags = slfn.Contains(".tag");
1304 if (slfn.Contains(".root")) msg += " type: root file;";
f866cba5 1305 else msg += " type: unknown file;";
c57f56b7 1306 if (use_tags) msg += " using_tags: Yes";
1307 else msg += " using_tags: No";
1308 Info("CheckDataType", msg.Data());
1309}
1310
4e5c5506 1311//______________________________________________________________________________
1312void AliAnalysisAlien::EnablePackage(const char *package)
1313{
1314// Enables a par file supposed to exist in the current directory.
1315 TString pkg(package);
1316 pkg.ReplaceAll(".par", "");
1317 pkg += ".par";
1318 if (gSystem->AccessPathName(pkg)) {
ebcdf05e 1319 Fatal("EnablePackage", "Package %s not found", pkg.Data());
4e5c5506 1320 return;
1321 }
1322 if (!TObject::TestBit(AliAnalysisGrid::kUsePars))
1323 Info("EnablePackage", "AliEn plugin will use .par packages");
1324 TObject::SetBit(AliAnalysisGrid::kUsePars, kTRUE);
1325 if (!fPackages) {
1326 fPackages = new TObjArray();
1327 fPackages->SetOwner();
1328 }
1329 fPackages->Add(new TObjString(pkg));
1330}
1331
d2a409b2 1332//______________________________________________________________________________
1333const char *AliAnalysisAlien::GetJobStatus(Int_t jobidstart, Int_t lastid, Int_t &nrunning, Int_t &nwaiting, Int_t &nerror, Int_t &ndone)
1334{
1335// Get job status for all jobs with jobid>jobidstart.
1336 static char mstatus[20];
1337 mstatus[0] = '\0';
1338 nrunning = 0;
1339 nwaiting = 0;
1340 nerror = 0;
1341 ndone = 0;
1342 TGridJobStatusList *list = gGrid->Ps("");
1343 if (!list) return mstatus;
1344 Int_t nentries = list->GetSize();
1345 TGridJobStatus *status;
1346 Int_t pid;
1347 for (Int_t ijob=0; ijob<nentries; ijob++) {
1348 status = (TGridJobStatus *)list->At(ijob);
1349 pid = gROOT->ProcessLine(Form("atoi(((TAlienJobStatus*)0x%lx)->GetKey(\"queueId\"));", (ULong_t)status));
1350 if (pid<jobidstart) continue;
1351 if (pid == lastid) {
1352 gROOT->ProcessLine(Form("sprintf((char*)0x%lx,((TAlienJobStatus*)0x%lx)->GetKey(\"status\"));",(ULong_t)mstatus, (ULong_t)status));
1353 }
1354 switch (status->GetStatus()) {
1355 case TGridJobStatus::kWAITING:
1356 nwaiting++; break;
1357 case TGridJobStatus::kRUNNING:
1358 nrunning++; break;
1359 case TGridJobStatus::kABORTED:
1360 case TGridJobStatus::kFAIL:
1361 case TGridJobStatus::kUNKNOWN:
1362 nerror++; break;
1363 case TGridJobStatus::kDONE:
1364 ndone++;
1365 }
1366 }
1367 list->Delete();
1368 delete list;
1369 return mstatus;
1370}
1371
c57f56b7 1372//______________________________________________________________________________
1373Bool_t AliAnalysisAlien::IsCollection(const char *lfn) const
1374{
1375// Returns true if file is a collection. Functionality duplicated from
1376// TAlien::Type() because we don't want to directly depend on TAlien.
1377 if (!gGrid) {
1378 Error("IsCollection", "No connection to grid");
1379 return kFALSE;
1380 }
1381 TGridResult *res = gGrid->Command(Form("type -z %s",lfn),kFALSE);
1382 if (!res) return kFALSE;
1383 const char* typeStr = res->GetKey(0, "type");
1384 if (!typeStr || !strlen(typeStr)) return kFALSE;
1385 if (!strcmp(typeStr, "collection")) return kTRUE;
1386 delete res;
1387 return kFALSE;
1388}
1389
fe2d7fc2 1390//______________________________________________________________________________
1391Bool_t AliAnalysisAlien::IsSingleOutput() const
1392{
1393// Check if single-ouput option is on.
1394 return (!fOutputSingle.IsNull());
1395}
1396
16a4353c 1397//______________________________________________________________________________
1398void AliAnalysisAlien::Print(Option_t *) const
1399{
1400// Print current plugin settings.
84fcd93f 1401 printf("### AliEn analysis plugin current settings ###\n");
1402 printf("= Production mode:______________________________ %d\n", fProductionMode);
1403 printf("= Version of API requested: ____________________ %s\n", fAPIVersion.Data());
1404 printf("= Version of ROOT requested: ___________________ %s\n", fROOTVersion.Data());
1405 printf("= Version of AliRoot requested: ________________ %s\n", fAliROOTVersion.Data());
16a4353c 1406 if (fUser.Length())
84fcd93f 1407 printf("= User running the plugin: _____________________ %s\n", fUser.Data());
1408 printf("= Grid workdir relative to user $HOME: _________ %s\n", fGridWorkingDir.Data());
1409 printf("= Grid output directory relative to workdir: ___ %s\n", fGridOutputDir.Data());
1410 printf("= Data base directory path requested: __________ %s\n", fGridDataDir.Data());
1411 printf("= Data search pattern: _________________________ %s\n", fDataPattern.Data());
1412 printf("= Input data format: ___________________________ %s\n", fInputFormat.Data());
16a4353c 1413 if (fRunNumbers.Length())
84fcd93f 1414 printf("= Run numbers to be processed: _________________ %s\n", fRunNumbers.Data());
16a4353c 1415 if (fRunRange[0])
5fce53f4 1416 printf("= Run range to be processed: ___________________ %s%d-%s%d\n", fRunPrefix.Data(), fRunRange[0], fRunPrefix.Data(), fRunRange[1]);
16a4353c 1417 if (!fRunRange[0] && !fRunNumbers.Length()) {
1418 TIter next(fInputFiles);
1419 TObject *obj;
1420 TString list;
1421 while ((obj=next())) list += obj->GetName();
84fcd93f 1422 printf("= Input files to be processed: _________________ %s\n", list.Data());
16a4353c 1423 }
1424 if (TestBit(AliAnalysisGrid::kTest))
84fcd93f 1425 printf("= Number of input files used in test mode: _____ %d\n", fNtestFiles);
1426 printf("= List of output files to be registered: _______ %s\n", fOutputFiles.Data());
1427 printf("= List of outputs going to be archived: ________ %s\n", fOutputArchive.Data());
1428 printf("= List of outputs that should not be merged: ___ %s\n", fMergeExcludes.Data());
1429 printf("=====================================================================\n");
1430 printf("= Job price: ___________________________________ %d\n", fPrice);
1431 printf("= Time to live (TTL): __________________________ %d\n", fTTL);
1432 printf("= Max files per subjob: ________________________ %d\n", fSplitMaxInputFileNumber);
16a4353c 1433 if (fMaxInitFailed>0)
84fcd93f 1434 printf("= Max number of subjob fails to kill: __________ %d\n", fMaxInitFailed);
16a4353c 1435 if (fMasterResubmitThreshold>0)
84fcd93f 1436 printf("= Resubmit master job if failed subjobs >_______ %d\n", fMasterResubmitThreshold);
319593fb 1437 if (fNrunsPerMaster>0)
84fcd93f 1438 printf("= Number of runs per master job: _______________ %d\n", fNrunsPerMaster);
1439 printf("= Number of files in one chunk to be merged: ___ %d\n", fMaxMergeFiles);
b5b9dee8 1440 printf("= Name of the generated execution script: ______ %s\n", fExecutable.Data());
1441 printf("= Executable command: __________________________ %s\n", fExecutableCommand.Data());
16a4353c 1442 if (fArguments.Length())
84fcd93f 1443 printf("= Arguments for the execution script: __________ %s\n",fArguments.Data());
631c0b05 1444 if (fExecutableArgs.Length())
1445 printf("= Arguments after macro name in executable______ %s\n",fExecutableArgs.Data());
84fcd93f 1446 printf("= Name of the generated analysis macro: ________ %s\n",fAnalysisMacro.Data());
1447 printf("= User analysis files to be deployed: __________ %s\n",fAnalysisSource.Data());
1448 printf("= Additional libs to be loaded or souces to be compiled runtime: <%s>\n",fAdditionalLibs.Data());
1449 printf("= Master jobs split mode: ______________________ %s\n",fSplitMode.Data());
16a4353c 1450 if (fDatasetName)
84fcd93f 1451 printf("= Custom name for the dataset to be created: ___ %s\n", fDatasetName.Data());
1452 printf("= Name of the generated JDL: ___________________ %s\n", fJDLName.Data());
16a4353c 1453 if (fIncludePath.Data())
84fcd93f 1454 printf("= Include path for runtime task compilation: ___ %s\n", fIncludePath.Data());
16a4353c 1455 if (fCloseSE.Length())
84fcd93f 1456 printf("= Force job outputs to storage element: ________ %s\n", fCloseSE.Data());
16a4353c 1457 if (fFriendChainName.Length())
84fcd93f 1458 printf("= Open friend chain file on worker: ____________ %s\n", fFriendChainName.Data());
16a4353c 1459 if (fPackages) {
1460 TIter next(fPackages);
1461 TObject *obj;
1462 TString list;
1463 while ((obj=next())) list += obj->GetName();
84fcd93f 1464 printf("= Par files to be used: ________________________ %s\n", list.Data());
16a4353c 1465 }
1466}
1467
c57f56b7 1468//______________________________________________________________________________
1469void AliAnalysisAlien::SetDefaults()
1470{
1471// Set default values for everything. What cannot be filled will be left empty.
1472 if (fGridJDL) delete fGridJDL;
1473 fGridJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
0f389141 1474 fMergingJDL = (TGridJDL*)gROOT->ProcessLine("new TAlienJDL()");
c57f56b7 1475 fPrice = 1;
1476 fTTL = 30000;
1477 fSplitMaxInputFileNumber = 100;
1478 fMaxInitFailed = 0;
1479 fMasterResubmitThreshold = 0;
bb885a9e 1480 fNtestFiles = 10;
a8739e8a 1481 fRunRange[0] = 0;
1482 fRunRange[1] = 0;
319593fb 1483 fNrunsPerMaster = 1;
16a4353c 1484 fMaxMergeFiles = 100;
c57f56b7 1485 fRunNumbers = "";
1486 fExecutable = "analysis.sh";
0a1c1f7f 1487 fExecutableCommand = "root -b -q";
c57f56b7 1488 fArguments = "";
631c0b05 1489 fExecutableArgs = "";
c57f56b7 1490 fAnalysisMacro = "myAnalysis.C";
1491 fAnalysisSource = "";
1492 fAdditionalLibs = "";
1493 fSplitMode = "se";
1494 fAPIVersion = "";
1495 fROOTVersion = "";
1496 fAliROOTVersion = "";
1497 fUser = ""; // Your alien user name
1498 fGridWorkingDir = "";
1499 fGridDataDir = ""; // Can be like: /alice/sim/PDC_08a/LHC08c9/
1500 fDataPattern = "*AliESDs.root"; // Can be like: *AliESDs.root, */pass1/*AliESDs.root, ...
0df6ccf2 1501 fFriendChainName = "";
c57f56b7 1502 fGridOutputDir = "output";
1503 fOutputArchive = "log_archive.zip:stdout,stderr root_archive.zip:*.root";
1504 fOutputFiles = ""; // Like "AliAODs.root histos.root"
1505 fInputFormat = "xml-single";
1506 fJDLName = "analysis.jdl";
c6cb3634 1507 fJobTag = "Automatically generated analysis JDL";
bb885a9e 1508 fMergeExcludes = "";
0f389141 1509 fMergeViaJDL = 0;
c57f56b7 1510}
1511
0f389141 1512//______________________________________________________________________________
1513Bool_t AliAnalysisAlien::MergeOutput(const char *output, const char *basedir, Int_t nmaxmerge)
1514{
1515// Merge all registered outputs from basedir.
1516 TString output_file = output;
1517 TString command;
1518 TString output_chunk;
1519 TString previous_chunk = "";
1520 Int_t count_chunk = 0;
1521 Int_t count_zero = nmaxmerge;
1522 Bool_t merged = kTRUE;
1523 Int_t index = output_file.Index("@");
1524 if (index > 0) output_file.Remove(index);
1525 command = Form("find %s/ *%s", basedir, output_file.Data());
1526 printf("command: %s\n", command.Data());
1527 TGridResult *res = gGrid->Command(command);
1528 if (!res) {
1529 printf("Error: No result for the find command\n");
1530 return kFALSE;
1531 }
1532
1533 TFileMerger *fm = 0;
1534 TIter nextmap(res);
1535 TMap *map = 0;
1536 // Check if there is a merge operation to resume
1537 output_chunk = output_file;
1538 output_chunk.ReplaceAll(".root", "_*.root");
1539 // Check for existent temporary merge files
1540 if (!gSystem->Exec(Form("ls %s", output_chunk.Data()))) {
1541 while (1) {
1542 // Skip as many input files as in a chunk
1543 for (Int_t counter=0; counter<nmaxmerge; counter++) map = (TMap*)nextmap();
1544 if (!map) {
1545 ::Error("MergeOutputs", "Cannot resume merging for <%s>, nentries=%d", output_file.Data(), res->GetSize());
1546 delete res;
1547 return kFALSE;
1548 }
1549 output_chunk = output_file;
1550 output_chunk.ReplaceAll(".root", Form("_%04d.root", count_chunk));
1551 count_chunk++;
1552 if (gSystem->AccessPathName(output_chunk)) continue;
1553 // Merged file with chunks up to <count_chunk> found
1554 printf("Resume merging of <%s> from <%s>\n", output_file.Data(), output_chunk.Data());
1555 previous_chunk = output_chunk;
1556 break;
1557 }
1558 }
1559 count_zero = nmaxmerge;
1560
1561 while ((map=(TMap*)nextmap())) {
1562 // Loop 'find' results and get next LFN
1563 if (count_zero == nmaxmerge) {
1564 // First file in chunk - create file merger and add previous chunk if any.
1565 fm = new TFileMerger(kFALSE);
1566 fm->SetFastMethod(kTRUE);
1567 if (previous_chunk.Length()) fm->AddFile(previous_chunk.Data());
1568 output_chunk = output_file;
1569 output_chunk.ReplaceAll(".root", Form("_%04d.root", count_chunk));
1570 }
1571 // If last file found, put merged results in the output file
1572 if (map == res->Last()) output_chunk = output_file;
1573 TObjString *objs = dynamic_cast<TObjString*>(map->GetValue("turl"));
1574 if (!objs || !objs->GetString().Length()) {
1575 // Nothing found - skip this output
1576 delete res;
1577 delete fm;
1578 return kFALSE;
1579 }
1580 // Add file to be merged and decrement chunk counter.
1581 fm->AddFile(objs->GetString());
1582 count_zero--;
1583 if (count_zero==0 || map == res->Last()) {
1584 fm->OutputFile(output_chunk);
1585 if (!fm->GetMergeList() || !fm->GetMergeList()->GetSize()) {
1586 // Nothing found - skip this output
1587 ::Warning("MergeOutputs", "No <%s> files found.", output_file.Data());
1588 delete res;
1589 delete fm;
1590 return kFALSE;
1591 }
1592 // Merge the outputs, then go to next chunk
1593 if (!fm->Merge()) {
1594 ::Error("MergeOutputs", "Could not merge all <%s> files", output_file.Data());
1595 delete res;
1596 delete fm;
1597 merged = kFALSE;
1598 return kFALSE;
1599 } else {
1600 ::Info("MergeOutputs", "\n##### Merged %d output files to <%s>", fm->GetMergeList()->GetSize(), output_chunk.Data());
1601 gSystem->Unlink(previous_chunk);
1602 }
1603 if (map == res->Last()) {
1604 delete res;
1605 delete fm;
1606 break;
1607 }
1608 count_chunk++;
1609 count_zero = nmaxmerge;
1610 previous_chunk = output_chunk;
1611 }
1612 }
1613 return merged;
1614}
1615
c57f56b7 1616//______________________________________________________________________________
1617Bool_t AliAnalysisAlien::MergeOutputs()
1618{
1619// Merge analysis outputs existing in the AliEn space.
1620 if (TestBit(AliAnalysisGrid::kTest)) return kTRUE;
1621 if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE;
1622 if (!Connect()) {
1623 Error("MergeOutputs", "Cannot merge outputs without grid connection. Terminate will NOT be executed");
1624 return kFALSE;
0f389141 1625 }
c9e8f7fd 1626 if (fMergeViaJDL) {
1627 if (!TestBit(AliAnalysisGrid::kMerge)) {
1628 Info("MergeOutputs", "### Re-run with <MergeViaJDL> option in terminate mode of the plugin to submit merging jobs ###");
1629 return kFALSE;
1630 }
1631 if (fProductionMode) {
1632 Info("MergeOutputs", "### Merging will be submitted by LPM manager... ###");
1633 return kFALSE;
1634 }
0f389141 1635 Info("MergeOutputs", "Submitting merging JDL");
1636 SubmitMerging();
1637 Info("MergeOutputs", "### Re-run with <MergeViaJDL> off to collect results after merging jobs are done ###");
c9e8f7fd 1638 Info("MergeOutputs", "### The Terminate() method is executed by the merging jobs");
001cb79e 1639 return kFALSE;
c57f56b7 1640 }
1641 // Get the output path
d2a409b2 1642 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
923e2ca5 1643 if (!DirectoryExists(fGridOutputDir)) {
c57f56b7 1644 Error("MergeOutputs", "Grid output directory %s not found. Terminate() will NOT be executed", fGridOutputDir.Data());
1645 return kFALSE;
1646 }
1647 if (!fOutputFiles.Length()) {
1648 Error("MergeOutputs", "No output file names defined. Are you running the right AliAnalysisAlien configuration ?");
1649 return kFALSE;
0f389141 1650 }
1651 // Check if fast read option was requested
1652 if (fFastReadOption) {
1653 Warning("MergeOutputs", "You requested FastRead option. Using xrootd flags to reduce timeouts. Note that this may skip some files that could be accessed !");
1654 gEnv->SetValue("XNet.ConnectTimeout",5);
1655 gEnv->SetValue("XNet.RequestTimeout",5);
1656 gEnv->SetValue("XNet.MaxRedirectCount",2);
1657 gEnv->SetValue("XNet.ReconnectTimeout",5);
1658 gEnv->SetValue("XNet.FirstConnectMaxCnt",1);
c57f56b7 1659 }
1660 TObjArray *list = fOutputFiles.Tokenize(" ");
1661 TIter next(list);
1662 TObjString *str;
c57f56b7 1663 TString output_file;
1664 Bool_t merged = kTRUE;
1665 while((str=(TObjString*)next())) {
1666 output_file = str->GetString();
1667 Int_t index = output_file.Index("@");
1668 if (index > 0) output_file.Remove(index);
319593fb 1669 // Skip already merged outputs
1670 if (!gSystem->AccessPathName(output_file)) {
1671 Info("MergeOutputs", "Output file <%s> found. Not merging again.", output_file.Data());
1672 continue;
1673 }
bb885a9e 1674 if (fMergeExcludes.Length() &&
1675 fMergeExcludes.Contains(output_file.Data())) continue;
16a4353c 1676 // Perform a 'find' command in the output directory, looking for registered outputs
0f389141 1677 merged = MergeOutput(output_file, fGridOutputDir, fMaxMergeFiles);
1678 if (!merged) {
1679 Error("MergeOutputs", "Terminate() will NOT be executed");
1680 return kFALSE;
1681 }
c57f56b7 1682 }
0f389141 1683 return kTRUE;
c57f56b7 1684}
1685
bb885a9e 1686//______________________________________________________________________________
1687void AliAnalysisAlien::SetDefaultOutputs(Bool_t flag)
1688{
1689// Use the output files connected to output containers from the analysis manager
1690// rather than the files defined by SetOutputFiles
1691 if (flag && !TObject::TestBit(AliAnalysisGrid::kDefaultOutputs))
1692 Info("SetDefaultOutputs", "Plugin will use the output files taken from \
1693 analysis manager");
1694 TObject::SetBit(AliAnalysisGrid::kDefaultOutputs, flag);
1695}
1696
5513444a 1697//______________________________________________________________________________
1698Bool_t AliAnalysisAlien::StartAnalysis(Long64_t /*nentries*/, Long64_t /*firstEntry*/)
c57f56b7 1699{
1700// Start remote grid analysis.
1701
43da816a 1702 // Check if output files have to be taken from the analysis manager
1703 if (TestBit(AliAnalysisGrid::kDefaultOutputs)) {
1704 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
1705 if (!mgr || !mgr->IsInitialized()) {
1706 Error("StartAnalysis", "You need an initialized analysis manager for this");
5513444a 1707 return kFALSE;
43da816a 1708 }
1709 fOutputFiles = "";
1710 TIter next(mgr->GetOutputs());
1711 AliAnalysisDataContainer *output;
1712 while ((output=(AliAnalysisDataContainer*)next())) {
1713 const char *filename = output->GetFileName();
1714 if (!(strcmp(filename, "default"))) {
1715 if (!mgr->GetOutputEventHandler()) continue;
1716 filename = mgr->GetOutputEventHandler()->GetOutputFileName();
1717 }
84fcd93f 1718 if (fOutputFiles.Contains(filename)) continue;
43da816a 1719 if (fOutputFiles.Length()) fOutputFiles += " ";
1720 fOutputFiles += filename;
1721 }
c07b9ce2 1722 // Add extra files registered to the analysis manager
1723 if (mgr->GetExtraFiles().Length()) {
1724 if (fOutputFiles.Length()) fOutputFiles += " ";
1725 fOutputFiles += mgr->GetExtraFiles();
84fcd93f 1726 }
43da816a 1727 }
f7b1cbc2 1728// if (!fCloseSE.Length()) fCloseSE = gSystem->Getenv("alien_CLOSE_SE");
c57f56b7 1729 if (TestBit(AliAnalysisGrid::kOffline)) {
1730 Info("StartAnalysis","\n##### OFFLINE MODE ##### Files to be used in GRID are produced but not copied \
1731 \n there nor any job run. You can revise the JDL and analysis \
1732 \n macro then run the same in \"submit\" mode.");
1733 } else if (TestBit(AliAnalysisGrid::kTest)) {
1734 Info("StartAnalysis","\n##### LOCAL MODE ##### Your analysis will be run locally on a subset of the requested \
1735 \n dataset.");
1736 } else if (TestBit(AliAnalysisGrid::kSubmit)) {
1737 Info("StartAnalysis","\n##### SUBMIT MODE ##### Files required by your analysis are copied to your grid working \
1738 \n space and job submitted.");
1739 } else if (TestBit(AliAnalysisGrid::kMerge)) {
1740 Info("StartAnalysis","\n##### MERGE MODE ##### The registered outputs of the analysis will be merged");
0f389141 1741 if (fMergeViaJDL) CheckInputData();
5513444a 1742 return kTRUE;
c57f56b7 1743 } else {
1744 Info("StartAnalysis","\n##### FULL ANALYSIS MODE ##### Producing needed files and submitting your analysis job...");
1745 }
1746
1747 if (!Connect()) {
1748 Error("StartAnalysis", "Cannot start grid analysis without grid connection");
5513444a 1749 return kFALSE;
16a4353c 1750 }
1751 Print();
c57f56b7 1752 if (!CheckInputData()) {
1753 Error("StartAnalysis", "There was an error in preprocessing your requested input data");
5513444a 1754 return kFALSE;
c57f56b7 1755 }
1756 CreateDataset(fDataPattern);
1757 WriteAnalysisFile();
1758 WriteAnalysisMacro();
1759 WriteExecutable();
1760 WriteValidationScript();
0f389141 1761 if (fMergeViaJDL) {
1762 WriteMergingMacro();
1763 WriteMergeExecutable();
1764 WriteValidationScript(kTRUE);
1765 }
5513444a 1766 if (!CreateJDL()) return kFALSE;
1767 if (TestBit(AliAnalysisGrid::kOffline)) return kFALSE;
c57f56b7 1768 if (TestBit(AliAnalysisGrid::kTest)) {
1769 // Locally testing the analysis
1770 Info("StartAnalysis", "\n_______________________________________________________________________ \
1771 \n Running analysis script in a daughter shell as on a worker node \
1772 \n_______________________________________________________________________");
1773 TObjArray *list = fOutputFiles.Tokenize(" ");
1774 TIter next(list);
1775 TObjString *str;
1776 TString output_file;
1777 while((str=(TObjString*)next())) {
1778 output_file = str->GetString();
1779 Int_t index = output_file.Index("@");
1780 if (index > 0) output_file.Remove(index);
43da816a 1781 if (!gSystem->AccessPathName(output_file)) gSystem->Exec(Form("rm %s", output_file.Data()));
c57f56b7 1782 }
1783 delete list;
1784 gSystem->Exec(Form("bash %s 2>stderr", fExecutable.Data()));
0d5d317c 1785 TString validationScript = fExecutable;
1786 validationScript.ReplaceAll(".sh", "_validation.sh");
1787 gSystem->Exec(Form("bash %s",validationScript.Data()));
c57f56b7 1788// gSystem->Exec("cat stdout");
5513444a 1789 return kFALSE;
c57f56b7 1790 }
5513444a 1791 // Check if submitting is managed by LPM manager
a3e84053 1792 if (fProductionMode) {
5513444a 1793 TString prodfile = fJDLName;
1794 prodfile.ReplaceAll(".jdl", ".prod");
1795 WriteProductionFile(prodfile);
1796 Info("StartAnalysis", "Job submitting is managed by LPM. Rerun in terminate mode after jobs finished.");
1797 return kFALSE;
1798 }
a8739e8a 1799 // Submit AliEn job(s)
d2a409b2 1800 gGrid->Cd(fGridOutputDir);
a8739e8a 1801 TGridResult *res;
c57f56b7 1802 TString jobID = "";
d2a409b2 1803 if (!fRunNumbers.Length() && !fRunRange[0]) {
dd74a515 1804 // Submit a given xml or a set of runs
a8739e8a 1805 res = gGrid->Command(Form("submit %s", fJDLName.Data()));
84fcd93f 1806 printf("*************************** %s\n",Form("submit %s", fJDLName.Data()));
a8739e8a 1807 if (res) {
1808 const char *cjobId = res->GetKey(0,"jobId");
1809 if (!cjobId) {
1810 Error("StartAnalysis", "Your JDL %s could not be submitted", fJDLName.Data());
5513444a 1811 return kFALSE;
a8739e8a 1812 } else {
1813 Info("StartAnalysis", "\n_______________________________________________________________________ \
1814 \n##### Your JDL %s was successfully submitted. \nTHE JOB ID IS: %s \
1815 \n_______________________________________________________________________",
1816 fJDLName.Data(), cjobId);
1817 jobID = cjobId;
1818 }
1819 delete res;
1820 }
1821 } else {
d2a409b2 1822 // Submit for a range of enumeration of runs.
1823 Submit();
c57f56b7 1824 }
a8739e8a 1825
c57f56b7 1826 Info("StartAnalysis", "\n#### STARTING AN ALIEN SHELL FOR YOU. EXIT WHEN YOUR JOB %s HAS FINISHED. #### \
1827 \n You may exit at any time and terminate the job later using the option <terminate> \
1828 \n ##################################################################################", jobID.Data());
bb885a9e 1829 gSystem->Exec("aliensh");
5513444a 1830 return kTRUE;
c57f56b7 1831}
1832
d2a409b2 1833//______________________________________________________________________________
1834void AliAnalysisAlien::Submit()
1835{
1836// Submit all master jobs.
1837 Int_t nmasterjobs = fInputFiles->GetEntries();
1838 Long_t tshoot = gSystem->Now();
1839 if (!fNsubmitted) SubmitNext();
1840 while (fNsubmitted < nmasterjobs) {
1841 Long_t now = gSystem->Now();
1842 if ((now-tshoot)>30000) {
1843 tshoot = now;
1844 SubmitNext();
1845 }
1846 }
1847}
1848
0f389141 1849//______________________________________________________________________________
1850void AliAnalysisAlien::SubmitMerging()
1851{
1852// Submit all merging jobs.
1853 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
1854 gGrid->Cd(fGridOutputDir);
1855 TString mergeJDLName = fExecutable;
1856 mergeJDLName.ReplaceAll(".sh", "_merge.jdl");
1857 Int_t ntosubmit = fInputFiles->GetEntries();
1858 printf("### Submitting %d merging jobs...\n", ntosubmit);
1859 for (Int_t i=0; i<ntosubmit; i++) {
1860 TString query;
f866cba5 1861 TString runOutDir = gSystem->BaseName(fInputFiles->At(i)->GetName());
1862 runOutDir.ReplaceAll(".xml", "");
1863 if (fOutputToRunNo)
1864 query = Form("submit %s %s", mergeJDLName.Data(), runOutDir.Data());
1865 else
1866 query = Form("submit %s %03d", mergeJDLName.Data(), i);
0f389141 1867 printf("********* %s\n",query.Data());
1868 TGridResult *res = gGrid->Command(query);
1869 if (res) {
1870 const char *cjobId = res->GetKey(0,"jobId");
1871 if (!cjobId) {
1872 Error("StartAnalysis", "Your JDL %s could not be submitted", mergeJDLName.Data());
1873 return;
1874 } else {
1875 Info("StartAnalysis", "\n_______________________________________________________________________ \
1876 \n##### Your JDL %s was successfully submitted. \nTHE JOB ID IS: %s \
1877 \n_______________________________________________________________________",
1878 mergeJDLName.Data(), cjobId);
1879 }
1880 delete res;
1881 }
1882 }
1883 if (!ntosubmit) return;
1884 Info("StartAnalysis", "\n#### STARTING AN ALIEN SHELL FOR YOU. EXIT WHEN YOUR MERGING JOBS HAVE FINISHED. #### \
1885 \n You may exit at any time and terminate the job later using the option <terminate> but disabling SetMergeViaJDL\
1886 \n ##################################################################################");
1887 gSystem->Exec("aliensh");
1888}
1889
d2a409b2 1890//______________________________________________________________________________
1891void AliAnalysisAlien::SubmitNext()
1892{
1893// Submit next bunch of master jobs if the queue is free.
1894 static Bool_t iscalled = kFALSE;
1895 static Int_t firstmaster = 0;
1896 static Int_t lastmaster = 0;
1897 static Int_t npermaster = 0;
1898 if (iscalled) return;
1899 iscalled = kTRUE;
1900 Int_t nrunning=0, nwaiting=0, nerror=0, ndone=0;
1901 Int_t ntosubmit = 0;
1902 TGridResult *res;
1903 TString jobID = "";
1904 if (!fNsubmitted) ntosubmit = 1;
1905 else {
1906 TString status = GetJobStatus(firstmaster, lastmaster, nrunning, nwaiting, nerror, ndone);
84fcd93f 1907 printf("=== master %d: %s\n", lastmaster, status.Data());
d2a409b2 1908 // If last master not split, just return
1909 if (status != "SPLIT") {iscalled = kFALSE; return;}
1910 // No more than 100 waiting jobs
1911 if (nwaiting>100) {iscalled = kFALSE; return;}
1912 npermaster = (nrunning+nwaiting+nerror+ndone)/fNsubmitted;
1913 if (npermaster) ntosubmit = (100-nwaiting)/npermaster;
84fcd93f 1914 printf("=== WAITING(%d) RUNNING(%d) DONE(%d) OTHER(%d) NperMaster=%d => to submit %d jobs\n",
d2a409b2 1915 nwaiting, nrunning, ndone, nerror, npermaster, ntosubmit);
1916 }
1917 Int_t nmasterjobs = fInputFiles->GetEntries();
1918 for (Int_t i=0; i<ntosubmit; i++) {
1919 // Submit for a range of enumeration of runs.
1920 if (fNsubmitted>=nmasterjobs) {iscalled = kFALSE; return;}
1921 TString query;
cd11251e 1922 TString runOutDir = gSystem->BaseName(fInputFiles->At(fNsubmitted)->GetName());
1923 runOutDir.ReplaceAll(".xml", "");
1924 if (fOutputToRunNo)
1925 query = Form("submit %s %s %s", fJDLName.Data(), fInputFiles->At(fNsubmitted)->GetName(), runOutDir.Data());
1926 else
1927 query = Form("submit %s %s %03d", fJDLName.Data(), fInputFiles->At(fNsubmitted)->GetName(), fNsubmitted);
84fcd93f 1928 printf("********* %s\n",query.Data());
d2a409b2 1929 res = gGrid->Command(query);
1930 if (res) {
98ca124f 1931 TString cjobId1 = res->GetKey(0,"jobId");
1932 if (!cjobId1.Length()) {
d2a409b2 1933 Error("StartAnalysis", "Your JDL %s could not be submitted", fJDLName.Data());
1934 iscalled = kFALSE;
1935 return;
1936 } else {
1937 Info("StartAnalysis", "\n_______________________________________________________________________ \
1938 \n##### Your JDL %s submitted (%d to go). \nTHE JOB ID IS: %s \
1939 \n_______________________________________________________________________",
98ca124f 1940 fJDLName.Data(), nmasterjobs-fNsubmitted-1, cjobId1.Data());
d2a409b2 1941 jobID += cjobId1;
1942 jobID += " ";
98ca124f 1943 lastmaster = cjobId1.Atoi();
d2a409b2 1944 if (!firstmaster) firstmaster = lastmaster;
1945 fNsubmitted++;
1946 }
1947 delete res;
1948 }
1949 }
1950 iscalled = kFALSE;
1951}
1952
c57f56b7 1953//______________________________________________________________________________
1954void AliAnalysisAlien::WriteAnalysisFile()
1955{
f10e8481 1956// Write current analysis manager into the file <analysisFile>
1957 TString analysisFile = fExecutable;
1958 analysisFile.ReplaceAll(".sh", ".root");
c57f56b7 1959 if (!TestBit(AliAnalysisGrid::kSubmit)) {
1960 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
1961 if (!mgr || !mgr->IsInitialized()) {
1962 Error("WriteAnalysisFile", "You need an initialized analysis manager for this");
1963 return;
1964 }
1965 // Check analysis type
1966 TObject *handler;
1967 if (mgr->GetMCtruthEventHandler()) TObject::SetBit(AliAnalysisGrid::kUseMC);
1968 handler = (TObject*)mgr->GetInputEventHandler();
1969 if (handler) {
1970 if (handler->InheritsFrom("AliESDInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseESD);
1971 if (handler->InheritsFrom("AliAODInputHandler")) TObject::SetBit(AliAnalysisGrid::kUseAOD);
1972 }
1973 TDirectory *cdir = gDirectory;
f10e8481 1974 TFile *file = TFile::Open(analysisFile, "RECREATE");
c57f56b7 1975 if (file) {
fe2d7fc2 1976 // Skip task Terminate calls for the grid job
1977 mgr->SetSkipTerminate(kTRUE);
1978 // Unless merging makes no sense
1979 if (IsSingleOutput()) mgr->SetSkipTerminate(kFALSE);
c57f56b7 1980 mgr->Write();
1981 delete file;
fe2d7fc2 1982 // Enable termination for local jobs
1983 mgr->SetSkipTerminate(kFALSE);
c57f56b7 1984 }
1985 if (cdir) cdir->cd();
f10e8481 1986 Info("WriteAnalysisFile", "\n##### Analysis manager: %s wrote to file <%s>\n", mgr->GetName(),analysisFile.Data());
c57f56b7 1987 }
1988 Bool_t copy = kTRUE;
1989 if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
1990 if (copy) {
1991 CdWork();
1992 TString workdir = gGrid->GetHomeDirectory();
1993 workdir += fGridWorkingDir;
f10e8481 1994 Info("CreateJDL", "\n##### Copying file <%s> containing your initialized analysis manager to your alien workspace", analysisFile.Data());
1995 if (FileExists(analysisFile)) gGrid->Rm(analysisFile);
1996 TFile::Cp(Form("file:%s",analysisFile.Data()), Form("alien://%s/%s", workdir.Data(),analysisFile.Data()));
c57f56b7 1997 }
1998}
1999
2000//______________________________________________________________________________
2001void AliAnalysisAlien::WriteAnalysisMacro()
2002{
2003// Write the analysis macro that will steer the analysis in grid mode.
2004 if (!TestBit(AliAnalysisGrid::kSubmit)) {
2005 ofstream out;
2006 out.open(fAnalysisMacro.Data(), ios::out);
2007 if (!out.good()) {
2008 Error("WriteAnalysisMacro", "could not open file %s for writing", fAnalysisMacro.Data());
2009 return;
2010 }
5b273635 2011 Bool_t hasSTEERBase = kFALSE;
2012 Bool_t hasESD = kFALSE;
2013 Bool_t hasAOD = kFALSE;
2014 Bool_t hasANALYSIS = kFALSE;
2015 Bool_t hasANALYSISalice = kFALSE;
2016 Bool_t hasCORRFW = kFALSE;
c57f56b7 2017 TString func = fAnalysisMacro;
2018 TString type = "ESD";
2019 TString comment = "// Analysis using ";
2020 if (TObject::TestBit(AliAnalysisGrid::kUseESD)) comment += "ESD";
2021 if (TObject::TestBit(AliAnalysisGrid::kUseAOD)) {
2022 type = "AOD";
2023 comment += "AOD";
2024 }
0df6ccf2 2025 if (type!="AOD" && fFriendChainName!="") {
2026 Error("WriteAnalysisMacro", "Friend chain can be attached only to AOD");
2027 return;
2028 }
c57f56b7 2029 if (TObject::TestBit(AliAnalysisGrid::kUseMC)) comment += "/MC";
2030 else comment += " data";
2031 out << "const char *anatype = \"" << type.Data() << "\";" << endl << endl;
2032 func.ReplaceAll(".C", "");
2033 out << "void " << func.Data() << "()" << endl;
2034 out << "{" << endl;
2035 out << comment.Data() << endl;
2036 out << "// Automatically generated analysis steering macro executed in grid subjobs" << endl << endl;
f7498086 2037 out << " TStopwatch timer;" << endl;
2038 out << " timer.Start();" << endl << endl;
c57f56b7 2039 out << "// load base root libraries" << endl;
2040 out << " gSystem->Load(\"libTree\");" << endl;
2041 out << " gSystem->Load(\"libGeom\");" << endl;
2042 out << " gSystem->Load(\"libVMC\");" << endl;
2043 out << " gSystem->Load(\"libPhysics\");" << endl << endl;
648174cf 2044 out << " gSystem->Load(\"libMinuit\");" << endl << endl;
d5c6455a 2045 if (fAdditionalRootLibs.Length()) {
47a4137d 2046 // in principle libtree /lib geom libvmc etc. can go into this list, too
2047 out << "// Add aditional libraries" << endl;
2048 TObjArray *list = fAdditionalRootLibs.Tokenize(" ");
2049 TIter next(list);
2050 TObjString *str;
2051 while((str=(TObjString*)next())) {
2052 if (str->GetString().Contains(".so"))
2053 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
d5c6455a 2054 }
47a4137d 2055 if (list) delete list;
d5c6455a 2056 }
47a4137d 2057 out << "// include path" << endl;
2058 if (fIncludePath.Length()) out << " gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
2059 out << " gSystem->AddIncludePath(\"-I$ALICE_ROOT/include\");" << endl << endl;
57377eb5 2060 out << "// Load analysis framework libraries" << endl;
4e5c5506 2061 if (!fPackages) {
4e5c5506 2062 out << " gSystem->Load(\"libSTEERBase\");" << endl;
2063 out << " gSystem->Load(\"libESD\");" << endl;
2064 out << " gSystem->Load(\"libAOD\");" << endl;
2065 out << " gSystem->Load(\"libANALYSIS\");" << endl;
57377eb5 2066 out << " gSystem->Load(\"libANALYSISalice\");" << endl;
2067 out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
4e5c5506 2068 } else {
4e5c5506 2069 TIter next(fPackages);
2070 TObject *obj;
57377eb5 2071 TString pkgname;
5b273635 2072 TString setupPar = "AliAnalysisAlien::SetupPar";
57377eb5 2073 while ((obj=next())) {
2074 pkgname = obj->GetName();
4478e6f1 2075 if (pkgname == "STEERBase" ||
2076 pkgname == "STEERBase.par") hasSTEERBase = kTRUE;
2077 if (pkgname == "ESD" ||
2078 pkgname == "ESD.par") hasESD = kTRUE;
2079 if (pkgname == "AOD" ||
2080 pkgname == "AOD.par") hasAOD = kTRUE;
2081 if (pkgname == "ANALYSIS" ||
2082 pkgname == "ANALYSIS.par") hasANALYSIS = kTRUE;
2083 if (pkgname == "ANALYSISalice" ||
2084 pkgname == "ANALYSISalice.par") hasANALYSISalice = kTRUE;
2085 if (pkgname == "CORRFW" ||
2086 pkgname == "CORRFW.par") hasCORRFW = kTRUE;
5b273635 2087 }
2088 if (hasANALYSISalice) setupPar = "SetupPar";
57377eb5 2089 if (!hasSTEERBase) out << " gSystem->Load(\"libSTEERBase\");" << endl;
5b273635 2090 else out << " if (!" << setupPar << "(\"STEERBase\")) return;" << endl;
57377eb5 2091 if (!hasESD) out << " gSystem->Load(\"libESD\");" << endl;
5b273635 2092 else out << " if (!" << setupPar << "(\"ESD\")) return;" << endl;
57377eb5 2093 if (!hasAOD) out << " gSystem->Load(\"libAOD\");" << endl;
5b273635 2094 else out << " if (!" << setupPar << "(\"AOD\")) return;" << endl;
57377eb5 2095 if (!hasANALYSIS) out << " gSystem->Load(\"libANALYSIS\");" << endl;
5b273635 2096 else out << " if (!" << setupPar << "(\"ANALYSIS\")) return;" << endl;
57377eb5 2097 if (!hasANALYSISalice) out << " gSystem->Load(\"libANALYSISalice\");" << endl;
5b273635 2098 else out << " if (!" << setupPar << "(\"ANALYSISalice\")) return;" << endl;
57377eb5 2099 if (!hasCORRFW) out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
5b273635 2100 else out << " if (!" << setupPar << "(\"CORRFW\")) return;" << endl << endl;
57377eb5 2101 out << "// Compile other par packages" << endl;
2102 next.Reset();
fcc9bb6f 2103 while ((obj=next())) {
2104 pkgname = obj->GetName();
4478e6f1 2105 if (pkgname == "STEERBase" ||
2106 pkgname == "STEERBase.par" ||
2107 pkgname == "ESD" ||
2108 pkgname == "ESD.par" ||
2109 pkgname == "AOD" ||
2110 pkgname == "AOD.par" ||
2111 pkgname == "ANALYSIS" ||
2112 pkgname == "ANALYSIS.par" ||
2113 pkgname == "ANALYSISalice" ||
2114 pkgname == "ANALYSISalice.par" ||
2115 pkgname == "CORRFW" ||
2116 pkgname == "CORRFW.par") continue;
5b273635 2117 out << " if (!" << setupPar << "(\"" << obj->GetName() << "\")) return;" << endl;
fcc9bb6f 2118 }
4e5c5506 2119 }
6da75e0b 2120 if (fAdditionalLibs.Length()) {
2121 out << "// Add aditional AliRoot libraries" << endl;
2122 TObjArray *list = fAdditionalLibs.Tokenize(" ");
2123 TIter next(list);
2124 TObjString *str;
2125 while((str=(TObjString*)next())) {
2126 if (str->GetString().Contains(".so"))
2127 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
2128 }
2129 if (list) delete list;
2130 }
2131 out << endl;
c57f56b7 2132 out << "// analysis source to be compiled at runtime (if any)" << endl;
2133 if (fAnalysisSource.Length()) {
2134 TObjArray *list = fAnalysisSource.Tokenize(" ");
2135 TIter next(list);
2136 TObjString *str;
2137 while((str=(TObjString*)next())) {
2138 out << " gROOT->ProcessLine(\".L " << str->GetString().Data() << "+g\");" << endl;
2139 }
2140 if (list) delete list;
2141 }
2142 out << endl;
0f389141 2143 if (fFastReadOption) {
2144 Warning("WriteAnalysisMacro", "!!! You requested FastRead option. Using xrootd flags to reduce timeouts in the grid jobs. Note that this may skip some files that could be accessed !!!");
2145 out << "// fast xrootd reading enabled" << endl;
2146 out << " printf(\"!!! You requested FastRead option. Using xrootd flags to reduce timeouts. Note that this may skip some files that could be accessed !!!\");" << endl;
2147 out << " gEnv->SetValue(\"XNet.ConnectTimeout\",5);" << endl;
2148 out << " gEnv->SetValue(\"XNet.RequestTimeout\",5);" << endl;
2149 out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
2150 out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",5);" << endl;
2151 out << " gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl;
2152 }
c57f56b7 2153 out << "// connect to AliEn and make the chain" << endl;
2154 out << " if (!TGrid::Connect(\"alien://\")) return;" << endl;
2155 if (IsUsingTags()) {
2156 out << " TChain *chain = CreateChainFromTags(\"wn.xml\", anatype);" << endl << endl;
2157 } else {
76535c98 2158 if(fFriendChainName!="AliAOD.VertexingHF.root") {
2159 out << " TChain *chain = CreateChain(\"wn.xml\", anatype);" << endl << endl;
2160 } else {
2161 out << " // Check if the macro to create the chain was provided" << endl;
2162 out << " if (gSystem->AccessPathName(\"MakeAODInputChain.C\")) {" << endl;
2163 out << " ::Error(\"" << func.Data() << "\", \"File MakeAODInputChain.C not provided. Aborting.\");" << endl;
2164 out << " return;" << endl;
2165 out << " }" << endl;
2166 out << " gROOT->LoadMacro(\"MakeAODInputChain.C\");" << endl;
2167 out << " TChain *chain = MakeAODInputChain(\"wn.xml\",\"none\");" << endl << endl;
2168 }
c57f56b7 2169 }
2170 out << "// read the analysis manager from file" << endl;
f10e8481 2171 TString analysisFile = fExecutable;
2172 analysisFile.ReplaceAll(".sh", ".root");
2173 out << " TFile *file = TFile::Open(\"" << analysisFile << "\");" << endl;
c57f56b7 2174 out << " if (!file) return;" << endl;
2175 out << " TIter nextkey(file->GetListOfKeys());" << endl;
2176 out << " AliAnalysisManager *mgr = 0;" << endl;
2177 out << " TKey *key;" << endl;
2178 out << " while ((key=(TKey*)nextkey())) {" << endl;
2179 out << " if (!strcmp(key->GetClassName(), \"AliAnalysisManager\"))" << endl;
2180 out << " mgr = (AliAnalysisManager*)file->Get(key->GetName());" << endl;
2181 out << " };" << endl;
2182 out << " if (!mgr) {" << endl;
f10e8481 2183 out << " ::Error(\"" << func.Data() << "\", \"No analysis manager found in file" << analysisFile <<"\");" << endl;
c57f56b7 2184 out << " return;" << endl;
2185 out << " }" << endl << endl;
2186 out << " mgr->PrintStatus();" << endl;
52b6a92b 2187 if (AliAnalysisManager::GetAnalysisManager()) {
f866cba5 2188 if (AliAnalysisManager::GetAnalysisManager()->GetDebugLevel()>3) {
52b6a92b 2189 out << " gEnv->SetValue(\"XNet.Debug\", \"1\");" << endl;
de52b69c 2190 } else {
2191 out << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
52b6a92b 2192 }
2193 }
c57f56b7 2194 out << " mgr->StartAnalysis(\"localfile\", chain);" << endl;
f7498086 2195 out << " timer.Stop();" << endl;
2196 out << " timer.Print();" << endl;
c57f56b7 2197 out << "}" << endl << endl;
2198 if (IsUsingTags()) {
2199 out << "TChain* CreateChainFromTags(const char *xmlfile, const char *type=\"ESD\")" << endl;
2200 out << "{" << endl;
2201 out << "// Create a chain using tags from the xml file." << endl;
2202 out << " TAlienCollection* coll = TAlienCollection::Open(xmlfile);" << endl;
2203 out << " if (!coll) {" << endl;
2204 out << " ::Error(\"CreateChainFromTags\", \"Cannot create an AliEn collection from %s\", xmlfile);" << endl;
2205 out << " return NULL;" << endl;
2206 out << " }" << endl;
2207 out << " TGridResult* tagResult = coll->GetGridResult(\"\",kFALSE,kFALSE);" << endl;
2208 out << " AliTagAnalysis *tagAna = new AliTagAnalysis(type);" << endl;
2209 out << " tagAna->ChainGridTags(tagResult);" << endl << endl;
2210 out << " AliRunTagCuts *runCuts = new AliRunTagCuts();" << endl;
2211 out << " AliLHCTagCuts *lhcCuts = new AliLHCTagCuts();" << endl;
2212 out << " AliDetectorTagCuts *detCuts = new AliDetectorTagCuts();" << endl;
2213 out << " AliEventTagCuts *evCuts = new AliEventTagCuts();" << endl;
2214 out << " // Check if the cuts configuration file was provided" << endl;
2215 out << " if (!gSystem->AccessPathName(\"ConfigureCuts.C\")) {" << endl;
2216 out << " gROOT->LoadMacro(\"ConfigureCuts.C\");" << endl;
2217 out << " ConfigureCuts(runCuts, lhcCuts, detCuts, evCuts);" << endl;
2218 out << " }" << endl;
0df6ccf2 2219 if (fFriendChainName=="") {
2220 out << " TChain *chain = tagAna->QueryTags(runCuts, lhcCuts, detCuts, evCuts);" << endl;
2221 } else {
2222 out << " TString tmpColl=\"tmpCollection.xml\";" << endl;
2223 out << " tagAna->CreateXMLCollection(tmpColl.Data(),runCuts, lhcCuts, detCuts, evCuts);" << endl;
2224 out << " TChain *chain = CreateChain(tmpColl.Data(),type);" << endl;
2225 }
c57f56b7 2226 out << " if (!chain || !chain->GetNtrees()) return NULL;" << endl;
2227 out << " chain->ls();" << endl;
2228 out << " return chain;" << endl;
fcc9bb6f 2229 out << "}" << endl << endl;
c57f56b7 2230 if (gSystem->AccessPathName("ConfigureCuts.C")) {
2231 TString msg = "\n##### You may want to provide a macro ConfigureCuts.C with a method:\n";
2232 msg += " void ConfigureCuts(AliRunTagCuts *runCuts,\n";
2233 msg += " AliLHCTagCuts *lhcCuts,\n";
2234 msg += " AliDetectorTagCuts *detCuts,\n";
2235 msg += " AliEventTagCuts *evCuts)";
2236 Info("WriteAnalysisMacro", msg.Data());
2237 }
0df6ccf2 2238 }
2239 if (!IsUsingTags() || fFriendChainName!="") {
fcc9bb6f 2240 out <<"//________________________________________________________________________________" << endl;
c57f56b7 2241 out << "TChain* CreateChain(const char *xmlfile, const char *type=\"ESD\")" << endl;
2242 out << "{" << endl;
2243 out << "// Create a chain using url's from xml file" << endl;
2244 out << " TString treename = type;" << endl;
2245 out << " treename.ToLower();" << endl;
2246 out << " treename += \"Tree\";" << endl;
e02fee64 2247 out << " printf(\"***************************************\\n\");" << endl;
2248 out << " printf(\" Getting chain of trees %s\\n\", treename.Data());" << endl;
2249 out << " printf(\"***************************************\\n\");" << endl;
c57f56b7 2250 out << " TAlienCollection *coll = TAlienCollection::Open(xmlfile);" << endl;
2251 out << " if (!coll) {" << endl;
2252 out << " ::Error(\"CreateChain\", \"Cannot create an AliEn collection from %s\", xmlfile);" << endl;
2253 out << " return NULL;" << endl;
2254 out << " }" << endl;
2255 out << " TChain *chain = new TChain(treename);" << endl;
0df6ccf2 2256 if(fFriendChainName!="") {
2257 out << " TChain *chainFriend = new TChain(treename);" << endl;
2258 }
c57f56b7 2259 out << " coll->Reset();" << endl;
0df6ccf2 2260 out << " while (coll->Next()) {" << endl;
2261 out << " chain->Add(coll->GetTURL(\"\"));" << endl;
2262 if(fFriendChainName!="") {
2263 out << " TString fileFriend=coll->GetTURL(\"\");" << endl;
2264 out << " fileFriend.ReplaceAll(\"AliAOD.root\",\""<<fFriendChainName.Data()<<"\");" << endl;
2265 out << " fileFriend.ReplaceAll(\"AliAODs.root\",\""<<fFriendChainName.Data()<<"\");" << endl;
2266 out << " chainFriend->Add(fileFriend.Data());" << endl;
2267 }
2268 out << " }" << endl;
c57f56b7 2269 out << " if (!chain->GetNtrees()) {" << endl;
2270 out << " ::Error(\"CreateChain\", \"No tree found from collection %s\", xmlfile);" << endl;
2271 out << " return NULL;" << endl;
2272 out << " }" << endl;
0df6ccf2 2273 if(fFriendChainName!="") {
2274 out << " chain->AddFriend(chainFriend);" << endl;
2275 }
c57f56b7 2276 out << " return chain;" << endl;
fcc9bb6f 2277 out << "}" << endl << endl;
c57f56b7 2278 }
5b273635 2279 if (hasANALYSISalice) {
2280 out <<"//________________________________________________________________________________" << endl;
2281 out << "Bool_t SetupPar(const char *package) {" << endl;
2282 out << "// Compile the package and set it up." << endl;
2283 out << " TString pkgdir = package;" << endl;
2284 out << " pkgdir.ReplaceAll(\".par\",\"\");" << endl;
2285 out << " gSystem->Exec(Form(\"tar xvzf %s.par\", pkgdir.Data()));" << endl;
2286 out << " TString cdir = gSystem->WorkingDirectory();" << endl;
2287 out << " gSystem->ChangeDirectory(pkgdir);" << endl;
2288 out << " // Check for BUILD.sh and execute" << endl;
2289 out << " if (!gSystem->AccessPathName(\"PROOF-INF/BUILD.sh\")) {" << endl;
2290 out << " printf(\"*******************************\\n\");" << endl;
2291 out << " printf(\"*** Building PAR archive ***\\n\");" << endl;
2292 out << " printf(\"*******************************\\n\");" << endl;
2293 out << " if (gSystem->Exec(\"PROOF-INF/BUILD.sh\")) {" << endl;
2294 out << " ::Error(\"SetupPar\", \"Cannot build par archive %s\", pkgdir.Data());" << endl;
2295 out << " gSystem->ChangeDirectory(cdir);" << endl;
2296 out << " return kFALSE;" << endl;
2297 out << " }" << endl;
2298 out << " } else {" << endl;
2299 out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/BUILD.sh for package %s\", pkgdir.Data());" << endl;
2300 out << " gSystem->ChangeDirectory(cdir);" << endl;
2301 out << " return kFALSE;" << endl;
2302 out << " }" << endl;
2303 out << " // Check for SETUP.C and execute" << endl;
2304 out << " if (!gSystem->AccessPathName(\"PROOF-INF/SETUP.C\")) {" << endl;
2305 out << " printf(\"*******************************\\n\");" << endl;
2306 out << " printf(\"*** Setup PAR archive ***\\n\");" << endl;
2307 out << " printf(\"*******************************\\n\");" << endl;
2308 out << " gROOT->Macro(\"PROOF-INF/SETUP.C\");" << endl;
2309 out << " } else {" << endl;
2310 out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/SETUP.C for package %s\", pkgdir.Data());" << endl;
2311 out << " gSystem->ChangeDirectory(cdir);" << endl;
2312 out << " return kFALSE;" << endl;
2313 out << " }" << endl;
2314 out << " // Restore original workdir" << endl;
2315 out << " gSystem->ChangeDirectory(cdir);" << endl;
2316 out << " return kTRUE;" << endl;
2317 out << "}" << endl;
2318 }
c57f56b7 2319 Info("WriteAnalysisMacro", "\n##### Analysis macro to run on worker nodes <%s> written",fAnalysisMacro.Data());
2320 }
2321 Bool_t copy = kTRUE;
2322 if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
2323 if (copy) {
2324 CdWork();
2325 TString workdir = gGrid->GetHomeDirectory();
2326 workdir += fGridWorkingDir;
2327 if (FileExists(fAnalysisMacro)) gGrid->Rm(fAnalysisMacro);
2328 if (IsUsingTags() && !gSystem->AccessPathName("ConfigureCuts.C")) {
2329 if (FileExists("ConfigureCuts.C")) gGrid->Rm("ConfigureCuts.C");
2330 Info("WriteAnalysisMacro", "\n##### Copying cuts configuration macro: <ConfigureCuts.C> to your alien workspace");
2331 TFile::Cp("file:ConfigureCuts.C", Form("alien://%s/ConfigureCuts.C", workdir.Data()));
2332 }
2333 Info("WriteAnalysisMacro", "\n##### Copying analysis macro: <%s> to your alien workspace", fAnalysisMacro.Data());
2334 TFile::Cp(Form("file:%s",fAnalysisMacro.Data()), Form("alien://%s/%s", workdir.Data(), fAnalysisMacro.Data()));
2335 }
2336}
2337
0f389141 2338//______________________________________________________________________________
2339void AliAnalysisAlien::WriteMergingMacro()
2340{
2341// Write a macro to merge the outputs per master job.
2342 if (!fMergeViaJDL) return;
2343 if (!fOutputFiles.Length()) {
2344 Error("WriteMergingMacro", "No output file names defined. Are you running the right AliAnalysisAlien configuration ?");
2345 return;
2346 }
2347 TString mergingMacro = fExecutable;
2348 mergingMacro.ReplaceAll(".sh","_merge.C");
2349 if (!fGridOutputDir.Contains("/")) fGridOutputDir = Form("/%s/%s/%s", gGrid->GetHomeDirectory(), fGridWorkingDir.Data(), fGridOutputDir.Data());
2350 if (!TestBit(AliAnalysisGrid::kSubmit)) {
2351 ofstream out;
2352 out.open(mergingMacro.Data(), ios::out);
2353 if (!out.good()) {
2354 Error("WriteMergingMacro", "could not open file %s for writing", fAnalysisMacro.Data());
2355 return;
2356 }
5b273635 2357 Bool_t hasSTEERBase = kFALSE;
2358 Bool_t hasESD = kFALSE;
2359 Bool_t hasAOD = kFALSE;
2360 Bool_t hasANALYSIS = kFALSE;
2361 Bool_t hasANALYSISalice = kFALSE;
2362 Bool_t hasCORRFW = kFALSE;
0f389141 2363 TString func = mergingMacro;
2364 TString comment;
2365 func.ReplaceAll(".C", "");
2366 out << "void " << func.Data() << "(const char *dir)" << endl;
2367 out << "{" << endl;
2368 out << "// Automatically generated merging macro executed in grid subjobs" << endl << endl;
2369 out << " TStopwatch timer;" << endl;
2370 out << " timer.Start();" << endl << endl;
2371 out << "// load base root libraries" << endl;
2372 out << " gSystem->Load(\"libTree\");" << endl;
2373 out << " gSystem->Load(\"libGeom\");" << endl;
2374 out << " gSystem->Load(\"libVMC\");" << endl;
2375 out << " gSystem->Load(\"libPhysics\");" << endl << endl;
2376 out << " gSystem->Load(\"libMinuit\");" << endl << endl;
2377 if (fAdditionalRootLibs.Length()) {
2378 // in principle libtree /lib geom libvmc etc. can go into this list, too
2379 out << "// Add aditional libraries" << endl;
2380 TObjArray *list = fAdditionalRootLibs.Tokenize(" ");
2381 TIter next(list);
2382 TObjString *str;
2383 while((str=(TObjString*)next())) {
2384 if (str->GetString().Contains(".so"))
2385 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
2386 }
2387 if (list) delete list;
2388 }
2389 out << "// include path" << endl;
2390 if (fIncludePath.Length()) out << " gSystem->AddIncludePath(\"" << fIncludePath.Data() << "\");" << endl;
2391 out << " gSystem->AddIncludePath(\"-I$ALICE_ROOT/include\");" << endl << endl;
2392 out << "// Load analysis framework libraries" << endl;
2393 if (!fPackages) {
2394 out << " gSystem->Load(\"libSTEERBase\");" << endl;
2395 out << " gSystem->Load(\"libESD\");" << endl;
2396 out << " gSystem->Load(\"libAOD\");" << endl;
2397 out << " gSystem->Load(\"libANALYSIS\");" << endl;
2398 out << " gSystem->Load(\"libANALYSISalice\");" << endl;
2399 out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
2400 } else {
2401 TIter next(fPackages);
2402 TObject *obj;
2403 TString pkgname;
5b273635 2404 TString setupPar = "AliAnalysisAlien::SetupPar";
0f389141 2405 while ((obj=next())) {
2406 pkgname = obj->GetName();
2407 if (pkgname == "STEERBase" ||
2408 pkgname == "STEERBase.par") hasSTEERBase = kTRUE;
2409 if (pkgname == "ESD" ||
2410 pkgname == "ESD.par") hasESD = kTRUE;
2411 if (pkgname == "AOD" ||
2412 pkgname == "AOD.par") hasAOD = kTRUE;
2413 if (pkgname == "ANALYSIS" ||
2414 pkgname == "ANALYSIS.par") hasANALYSIS = kTRUE;
2415 if (pkgname == "ANALYSISalice" ||
2416 pkgname == "ANALYSISalice.par") hasANALYSISalice = kTRUE;
2417 if (pkgname == "CORRFW" ||
2418 pkgname == "CORRFW.par") hasCORRFW = kTRUE;
2419 }
5b273635 2420 if (hasANALYSISalice) setupPar = "SetupPar";
0f389141 2421 if (!hasSTEERBase) out << " gSystem->Load(\"libSTEERBase\");" << endl;
5b273635 2422 else out << " if (!" << setupPar << "(\"STEERBase\")) return;" << endl;
0f389141 2423 if (!hasESD) out << " gSystem->Load(\"libESD\");" << endl;
5b273635 2424 else out << " if (!" << setupPar << "(\"ESD\")) return;" << endl;
0f389141 2425 if (!hasAOD) out << " gSystem->Load(\"libAOD\");" << endl;
5b273635 2426 else out << " if (!" << setupPar << "(\"AOD\")) return;" << endl;
0f389141 2427 if (!hasANALYSIS) out << " gSystem->Load(\"libANALYSIS\");" << endl;
5b273635 2428 else out << " if (!" << setupPar << "(\"ANALYSIS\")) return;" << endl;
0f389141 2429 if (!hasANALYSISalice) out << " gSystem->Load(\"libANALYSISalice\");" << endl;
5b273635 2430 else out << " if (!" << setupPar << "(\"ANALYSISalice\")) return;" << endl;
0f389141 2431 if (!hasCORRFW) out << " gSystem->Load(\"libCORRFW\");" << endl << endl;
5b273635 2432 else out << " if (!" << setupPar << "(\"CORRFW\")) return;" << endl << endl;
0f389141 2433 out << "// Compile other par packages" << endl;
2434 next.Reset();
2435 while ((obj=next())) {
2436 pkgname = obj->GetName();
2437 if (pkgname == "STEERBase" ||
2438 pkgname == "STEERBase.par" ||
2439 pkgname == "ESD" ||
2440 pkgname == "ESD.par" ||
2441 pkgname == "AOD" ||
2442 pkgname == "AOD.par" ||
2443 pkgname == "ANALYSIS" ||
2444 pkgname == "ANALYSIS.par" ||
2445 pkgname == "ANALYSISalice" ||
2446 pkgname == "ANALYSISalice.par" ||
2447 pkgname == "CORRFW" ||
2448 pkgname == "CORRFW.par") continue;
5b273635 2449 out << " if (!" << setupPar << "(\"" << obj->GetName() << "\")) return;" << endl;
0f389141 2450 }
2451 }
2452 if (fAdditionalLibs.Length()) {
2453 out << "// Add aditional AliRoot libraries" << endl;
2454 TObjArray *list = fAdditionalLibs.Tokenize(" ");
2455 TIter next(list);
2456 TObjString *str;
2457 while((str=(TObjString*)next())) {
2458 if (str->GetString().Contains(".so"))
2459 out << " gSystem->Load(\"" << str->GetString().Data() << "\");" << endl;
2460 }
2461 if (list) delete list;
2462 }
2463 out << endl;
2464 out << "// Analysis source to be compiled at runtime (if any)" << endl;
2465 if (fAnalysisSource.Length()) {
2466 TObjArray *list = fAnalysisSource.Tokenize(" ");
2467 TIter next(list);
2468 TObjString *str;
2469 while((str=(TObjString*)next())) {
2470 out << " gROOT->ProcessLine(\".L " << str->GetString().Data() << "+g\");" << endl;
2471 }
2472 if (list) delete list;
2473 }
2474 out << endl;
2475 if (fFastReadOption) {
2476 Warning("WriteMergingMacro", "!!! You requested FastRead option. Using xrootd flags to reduce timeouts in the grid merging jobs. Note that this may skip some files that could be accessed !!!");
2477 out << "// fast xrootd reading enabled" << endl;
2478 out << " printf(\"!!! You requested FastRead option. Using xrootd flags to reduce timeouts. Note that this may skip some files that could be accessed !!!\");" << endl;
2479 out << " gEnv->SetValue(\"XNet.ConnectTimeout\",5);" << endl;
2480 out << " gEnv->SetValue(\"XNet.RequestTimeout\",5);" << endl;
2481 out << " gEnv->SetValue(\"XNet.MaxRedirectCount\",2);" << endl;
2482 out << " gEnv->SetValue(\"XNet.ReconnectTimeout\",5);" << endl;
2483 out << " gEnv->SetValue(\"XNet.FirstConnectMaxCnt\",1);" << endl << endl;
2484 }
2485 out << "// Connect to AliEn" << endl;
2486 out << " if (!TGrid::Connect(\"alien://\")) return;" << endl;
2487 out << " TString outputDir = \"" << fGridOutputDir << "/\";" << endl;
2488 out << " outputDir += dir;" << endl;
2489 out << " TString outputFiles = \"" << fOutputFiles << "\";" << endl;
2490 out << " TString mergeExcludes = \"" << fMergeExcludes << "\";" << endl;
1f0d1ca2 2491 out << " mergeExcludes += \"" << AliAnalysisManager::GetAnalysisManager()->GetExtraFiles() << "\";" << endl;
0f389141 2492 out << " TObjArray *list = outputFiles.Tokenize(\" \");" << endl;
2493 out << " TIter *iter = new TIter(list);" << endl;
2494 out << " TObjString *str;" << endl;
2495 out << " TString output_file;" << endl;
2496 out << " Bool_t merged = kTRUE;" << endl;
2497 out << " while((str=(TObjString*)iter->Next())) {" << endl;
2498 out << " output_file = str->GetString();" << endl;
2499 out << " Int_t index = output_file.Index(\"@\");" << endl;
2500 out << " if (index > 0) output_file.Remove(index);" << endl;
2501 out << " // Skip already merged outputs" << endl;
2502 out << " if (!gSystem->AccessPathName(output_file)) {" << endl;
2503 out << " printf(\"Output file <%s> found. Not merging again.\",output_file.Data());" << endl;
2504 out << " continue;" << endl;
2505 out << " }" << endl;
2506 out << " if (mergeExcludes.Contains(output_file.Data())) continue;" << endl;
2507 out << " merged = AliAnalysisAlien::MergeOutput(output_file, outputDir, " << fMaxMergeFiles << ");" << endl;
2508 out << " if (!merged) {" << endl;
2509 out << " printf(\"ERROR: Cannot merge %s\\n\", output_file.Data());" << endl;
0f389141 2510 out << " }" << endl;
2511 out << " }" << endl;
f866cba5 2512 out << "// read the analysis manager from file" << endl;
2513 TString analysisFile = fExecutable;
2514 analysisFile.ReplaceAll(".sh", ".root");
2515 out << " TFile *file = TFile::Open(\"" << analysisFile << "\");" << endl;
2516 out << " if (!file) return;" << endl;
2517 out << " TIter nextkey(file->GetListOfKeys());" << endl;
2518 out << " AliAnalysisManager *mgr = 0;" << endl;
2519 out << " TKey *key;" << endl;
2520 out << " while ((key=(TKey*)nextkey())) {" << endl;
2521 out << " if (!strcmp(key->GetClassName(), \"AliAnalysisManager\"))" << endl;
2522 out << " mgr = (AliAnalysisManager*)file->Get(key->GetName());" << endl;
2523 out << " };" << endl;
2524 out << " if (!mgr) {" << endl;
2525 out << " ::Error(\"" << func.Data() << "\", \"No analysis manager found in file" << analysisFile <<"\");" << endl;
2526 out << " return;" << endl;
2527 out << " }" << endl << endl;
b385fec0 2528 out << " mgr->SetSkipTerminate(kFALSE);" << endl;
f866cba5 2529 out << " mgr->PrintStatus();" << endl;
2530 if (AliAnalysisManager::GetAnalysisManager()) {
2531 if (AliAnalysisManager::GetAnalysisManager()->GetDebugLevel()>3) {
2532 out << " gEnv->SetValue(\"XNet.Debug\", \"1\");" << endl;
2533 } else {
2534 out << " AliLog::SetGlobalLogLevel(AliLog::kError);" << endl;
2535 }
2536 }
2537 out << " mgr->StartAnalysis(\"gridterminate\");" << endl;
0f389141 2538 out << "}" << endl << endl;
5b273635 2539 if (hasANALYSISalice) {
2540 out <<"//________________________________________________________________________________" << endl;
2541 out << "Bool_t SetupPar(const char *package) {" << endl;
2542 out << "// Compile the package and set it up." << endl;
2543 out << " TString pkgdir = package;" << endl;
2544 out << " pkgdir.ReplaceAll(\".par\",\"\");" << endl;
2545 out << " gSystem->Exec(Form(\"tar xvzf %s.par\", pkgdir.Data()));" << endl;
2546 out << " TString cdir = gSystem->WorkingDirectory();" << endl;
2547 out << " gSystem->ChangeDirectory(pkgdir);" << endl;
2548 out << " // Check for BUILD.sh and execute" << endl;
2549 out << " if (!gSystem->AccessPathName(\"PROOF-INF/BUILD.sh\")) {" << endl;
2550 out << " printf(\"*******************************\\n\");" << endl;
2551 out << " printf(\"*** Building PAR archive ***\\n\");" << endl;
2552 out << " printf(\"*******************************\\n\");" << endl;
2553 out << " if (gSystem->Exec(\"PROOF-INF/BUILD.sh\")) {" << endl;
2554 out << " ::Error(\"SetupPar\", \"Cannot build par archive %s\", pkgdir.Data());" << endl;
2555 out << " gSystem->ChangeDirectory(cdir);" << endl;
2556 out << " return kFALSE;" << endl;
2557 out << " }" << endl;
2558 out << " } else {" << endl;
2559 out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/BUILD.sh for package %s\", pkgdir.Data());" << endl;
2560 out << " gSystem->ChangeDirectory(cdir);" << endl;
2561 out << " return kFALSE;" << endl;
2562 out << " }" << endl;
2563 out << " // Check for SETUP.C and execute" << endl;
2564 out << " if (!gSystem->AccessPathName(\"PROOF-INF/SETUP.C\")) {" << endl;
2565 out << " printf(\"*******************************\\n\");" << endl;
2566 out << " printf(\"*** Setup PAR archive ***\\n\");" << endl;
2567 out << " printf(\"*******************************\\n\");" << endl;
2568 out << " gROOT->Macro(\"PROOF-INF/SETUP.C\");" << endl;
2569 out << " } else {" << endl;
2570 out << " ::Error(\"SetupPar\",\"Cannot access PROOF-INF/SETUP.C for package %s\", pkgdir.Data());" << endl;
2571 out << " gSystem->ChangeDirectory(cdir);" << endl;
2572 out << " return kFALSE;" << endl;
2573 out << " }" << endl;
2574 out << " // Restore original workdir" << endl;
2575 out << " gSystem->ChangeDirectory(cdir);" << endl;
2576 out << " return kTRUE;" << endl;
2577 out << "}" << endl;
2578 }
0f389141 2579 }
2580 Bool_t copy = kTRUE;
2581 if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
2582 if (copy) {
2583 CdWork();
2584 TString workdir = gGrid->GetHomeDirectory();
2585 workdir += fGridWorkingDir;
2586 if (FileExists(mergingMacro)) gGrid->Rm(mergingMacro);
2587 Info("WriteMergingMacro", "\n##### Copying merging macro: <%s> to your alien workspace", mergingMacro.Data());
2588 TFile::Cp(Form("file:%s",mergingMacro.Data()), Form("alien://%s/%s", workdir.Data(), mergingMacro.Data()));
2589 }
2590}
2591
2592//______________________________________________________________________________
2593Bool_t AliAnalysisAlien::SetupPar(const char *package)
2594{
2595// Compile the par file archive pointed by <package>. This must be present in the current durectory.
2596// Note that for loading the compiled library. The current directory should have precedence in
2597// LD_LIBRARY_PATH
2598 TString pkgdir = package;
2599 pkgdir.ReplaceAll(".par","");
2600 gSystem->Exec(Form("tar xvzf %s.par", pkgdir.Data()));
2601 TString cdir = gSystem->WorkingDirectory();
2602 gSystem->ChangeDirectory(pkgdir);
2603 // Check for BUILD.sh and execute
2604 if (!gSystem->AccessPathName("PROOF-INF/BUILD.sh")) {
2605 printf("**************************************************\n");
2606 printf("*** Building PAR archive %s\n", package);
2607 printf("**************************************************\n");
2608 if (gSystem->Exec("PROOF-INF/BUILD.sh")) {
2609 ::Error("SetupPar", "Cannot build par archive %s", pkgdir.Data());
2610 gSystem->ChangeDirectory(cdir);
2611 return kFALSE;
2612 }
2613 } else {
2614 ::Error("SetupPar","Cannot access PROOF-INF/BUILD.sh for package %s", pkgdir.Data());
2615 gSystem->ChangeDirectory(cdir);
2616 return kFALSE;
2617 }
2618 // Check for SETUP.C and execute
2619 if (!gSystem->AccessPathName("PROOF-INF/SETUP.C")) {
2620 printf("**************************************************\n");
2621 printf("*** Setup PAR archive %s\n", package);
2622 printf("**************************************************\n");
2623 gROOT->Macro("PROOF-INF/SETUP.C");
2624 printf("*** Loaded library: %s\n", gSystem->GetLibraries(pkgdir,"",kFALSE));
2625 } else {
2626 ::Error("SetupPar","Cannot access PROOF-INF/SETUP.C for package %s", pkgdir.Data());
2627 gSystem->ChangeDirectory(cdir);
2628 return kFALSE;
2629 }
2630 // Restore original workdir
2631 gSystem->ChangeDirectory(cdir);
2632 return kTRUE;
2633}
2634
c57f56b7 2635//______________________________________________________________________________
2636void AliAnalysisAlien::WriteExecutable()
2637{
2638// Generate the alien executable script.
2639 if (!TestBit(AliAnalysisGrid::kSubmit)) {
2640 ofstream out;
2641 out.open(fExecutable.Data(), ios::out);
2642 if (out.bad()) {
5513444a 2643 Error("WriteExecutable", "Bad file name for executable: %s", fExecutable.Data());
c57f56b7 2644 return;
2645 }
2646 out << "#!/bin/bash" << endl;
c57f56b7 2647 out << "echo \"=========================================\"" << endl;
2648 out << "echo \"############## PATH : ##############\"" << endl;
2649 out << "echo $PATH" << endl;
2650 out << "echo \"############## LD_LIBRARY_PATH : ##############\"" << endl;
2651 out << "echo $LD_LIBRARY_PATH" << endl;
2652 out << "echo \"############## ROOTSYS : ##############\"" << endl;
2653 out << "echo $ROOTSYS" << endl;
2654 out << "echo \"############## which root : ##############\"" << endl;
2655 out << "which root" << endl;
2656 out << "echo \"############## ALICE_ROOT : ##############\"" << endl;
2657 out << "echo $ALICE_ROOT" << endl;
2658 out << "echo \"############## which aliroot : ##############\"" << endl;
2659 out << "which aliroot" << endl;
9c5ddadc 2660 out << "echo \"############## system limits : ##############\"" << endl;
2661 out << "ulimit -a" << endl;
2662 out << "echo \"############## memory : ##############\"" << endl;
2663 out << "free -m" << endl;
c57f56b7 2664 out << "echo \"=========================================\"" << endl << endl;
74a53467 2665 // Make sure we can properly compile par files
2666 if (TObject::TestBit(AliAnalysisGrid::kUsePars)) out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
0a1c1f7f 2667 out << fExecutableCommand << " ";
631c0b05 2668 out << fAnalysisMacro.Data() << " " << fExecutableArgs.Data() << endl << endl;
9c5ddadc 2669 out << "echo \"======== " << fAnalysisMacro.Data() << " finished with exit code: $? ========\"" << endl;
2670 out << "echo \"############## memory after: ##############\"" << endl;
2671 out << "free -m" << endl;
2672 out << "echo \"############## Last 10 lines from dmesg : ##############\"" << endl;
2673 out << "dmesg | tail -n 10" << endl;
c57f56b7 2674 }
2675 Bool_t copy = kTRUE;
2676 if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
2677 if (copy) {
2678 CdWork();
2679 TString workdir = gGrid->GetHomeDirectory();
923e2ca5 2680 TString bindir = Form("%s/bin", workdir.Data());
2681 if (!DirectoryExists(bindir)) gGrid->Mkdir(bindir);
c57f56b7 2682 workdir += fGridWorkingDir;
2683 TString executable = Form("%s/bin/%s", gGrid->GetHomeDirectory(), fExecutable.Data());
2684 if (FileExists(executable)) gGrid->Rm(executable);
2685 Info("CreateJDL", "\n##### Copying executable file <%s> to your AliEn bin directory", fExecutable.Data());
2686 TFile::Cp(Form("file:%s",fExecutable.Data()), Form("alien://%s", executable.Data()));
2687 }
2688}
2689
0f389141 2690//______________________________________________________________________________
2691void AliAnalysisAlien::WriteMergeExecutable()
2692{
2693// Generate the alien executable script for the merging job.
2694 if (!fMergeViaJDL) return;
2695 TString mergeExec = fExecutable;
2696 mergeExec.ReplaceAll(".sh", "_merge.sh");
2697 if (!TestBit(AliAnalysisGrid::kSubmit)) {
2698 ofstream out;
2699 out.open(mergeExec.Data(), ios::out);
2700 if (out.bad()) {
2701 Error("WriteMergingExecutable", "Bad file name for executable: %s", mergeExec.Data());
2702 return;
2703 }
2704 out << "#!/bin/bash" << endl;
2705 out << "echo \"=========================================\"" << endl;
2706 out << "echo \"############## PATH : ##############\"" << endl;
2707 out << "echo $PATH" << endl;
2708 out << "echo \"############## LD_LIBRARY_PATH : ##############\"" << endl;
2709 out << "echo $LD_LIBRARY_PATH" << endl;
2710 out << "echo \"############## ROOTSYS : ##############\"" << endl;
2711 out << "echo $ROOTSYS" << endl;
2712 out << "echo \"############## which root : ##############\"" << endl;
2713 out << "which root" << endl;
2714 out << "echo \"############## ALICE_ROOT : ##############\"" << endl;
2715 out << "echo $ALICE_ROOT" << endl;
2716 out << "echo \"############## which aliroot : ##############\"" << endl;
2717 out << "which aliroot" << endl;
2718 out << "echo \"############## system limits : ##############\"" << endl;
2719 out << "ulimit -a" << endl;
2720 out << "echo \"############## memory : ##############\"" << endl;
2721 out << "free -m" << endl;
2722 out << "echo \"=========================================\"" << endl << endl;
2723 // Make sure we can properly compile par files
2724 if (TObject::TestBit(AliAnalysisGrid::kUsePars)) out << "export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH" << endl;
2725 TString mergeMacro = fExecutable;
2726 mergeMacro.ReplaceAll(".sh", "_merge.C");
2727 out << "export ARG=\"" << mergeMacro << "(\\\"$1\\\")\"" << endl;
2728 out << fExecutableCommand << " " << "$ARG" << endl;
2729 out << "echo \"======== " << mergeMacro.Data() << " finished with exit code: $? ========\"" << endl;
2730 out << "echo \"############## memory after: ##############\"" << endl;
2731 out << "free -m" << endl;
2732 out << "echo \"############## Last 10 lines from dmesg : ##############\"" << endl;
2733 out << "dmesg | tail -n 10" << endl;
2734 }
2735 Bool_t copy = kTRUE;
2736 if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
2737 if (copy) {
2738 CdWork();
2739 TString workdir = gGrid->GetHomeDirectory();
2740 TString bindir = Form("%s/bin", workdir.Data());
2741 if (!DirectoryExists(bindir)) gGrid->Mkdir(bindir);
2742 workdir += fGridWorkingDir;
2743 TString executable = Form("%s/bin/%s", gGrid->GetHomeDirectory(), mergeExec.Data());
2744 if (FileExists(executable)) gGrid->Rm(executable);
2745 Info("CreateJDL", "\n##### Copying executable file <%s> to your AliEn bin directory", mergeExec.Data());
2746 TFile::Cp(Form("file:%s",mergeExec.Data()), Form("alien://%s", executable.Data()));
2747 }
2748}
2749
c57f56b7 2750//______________________________________________________________________________
5513444a 2751void AliAnalysisAlien::WriteProductionFile(const char *filename) const
2752{
2753// Write the production file to be submitted by LPM manager. The format is:
f5e8c702 2754// First line: full_path_to_jdl estimated_no_subjobs_per_master
5513444a 2755// Next lines: full_path_to_dataset XXX (XXX is a string)
2756// To submit, one has to: submit jdl XXX for all lines
2757 ofstream out;
2758 out.open(filename, ios::out);
2759 if (out.bad()) {
2760 Error("WriteProductionFile", "Bad file name: %s", filename);
2761 return;
2762 }
2763 TString workdir = gGrid->GetHomeDirectory();
2764 workdir += fGridWorkingDir;
f5e8c702 2765 Int_t njobspermaster = 1000*fNrunsPerMaster/fSplitMaxInputFileNumber;
5513444a 2766 TString locjdl = Form("%s/%s", workdir.Data(),fJDLName.Data());
f5e8c702 2767 out << locjdl << " " << njobspermaster << endl;
5513444a 2768 Int_t nmasterjobs = fInputFiles->GetEntries();
2769 for (Int_t i=0; i<nmasterjobs; i++) {
409b4ada 2770 TString runOutDir = gSystem->BaseName(fInputFiles->At(i)->GetName());
2771 runOutDir.ReplaceAll(".xml", "");
2772 if (fOutputToRunNo)
2773 out << Form("%s", fInputFiles->At(i)->GetName()) << " " << runOutDir << endl;
2774 else
2775 out << Form("%s", fInputFiles->At(i)->GetName()) << " " << Form("%03d", i) << endl;
5513444a 2776 }
2777 Info("WriteProductionFile", "\n##### Copying production file <%s> to your work directory", filename);
fdbbc7be 2778 if (FileExists(filename)) gGrid->Rm(filename);
5513444a 2779 TFile::Cp(Form("file:%s",filename), Form("alien://%s/%s", workdir.Data(),filename));
2780}
2781
2782//______________________________________________________________________________
0f389141 2783void AliAnalysisAlien::WriteValidationScript(Bool_t merge)
c57f56b7 2784{
2785// Generate the alien validation script.
2786 // Generate the validation script
2787 TObjString *os;
0d5d317c 2788 TString validationScript = fExecutable;
0f389141 2789 if (merge) validationScript.ReplaceAll(".sh", "_mergevalidation.sh");
2790 else validationScript.ReplaceAll(".sh", "_validation.sh");
c57f56b7 2791 if (!Connect()) {
2792 Error("WriteValidationScript", "Alien connection required");
2793 return;
2794 }
2795 TString out_stream = "";
2796 if (!TestBit(AliAnalysisGrid::kTest)) out_stream = " >> stdout";
2797 if (!TestBit(AliAnalysisGrid::kSubmit)) {
2798 ofstream out;
0d5d317c 2799 out.open(validationScript, ios::out);
c57f56b7 2800 out << "#!/bin/bash" << endl;
2801 out << "##################################################" << endl;
2802 out << "validateout=`dirname $0`" << endl;
2803 out << "validatetime=`date`" << endl;
2804 out << "validated=\"0\";" << endl;
2805 out << "error=0" << endl;
2806 out << "if [ -z $validateout ]" << endl;
2807 out << "then" << endl;
2808 out << " validateout=\".\"" << endl;
2809 out << "fi" << endl << endl;
2810 out << "cd $validateout;" << endl;
2811 out << "validateworkdir=`pwd`;" << endl << endl;
2812 out << "echo \"*******************************************************\"" << out_stream << endl;
2813 out << "echo \"* Automatically generated validation script *\"" << out_stream << endl;
2814 out << "" << endl;
2815 out << "echo \"* Time: $validatetime \"" << out_stream << endl;
2816 out << "echo \"* Dir: $validateout\"" << out_stream << endl;
2817 out << "echo \"* Workdir: $validateworkdir\"" << out_stream << endl;
2818 out << "echo \"* ----------------------------------------------------*\"" << out_stream << endl;
2819 out << "ls -la ./" << out_stream << endl;
2820 out << "echo \"* ----------------------------------------------------*\"" << out_stream << endl << endl;
2821 out << "##################################################" << endl;
ebec370a 2822
2823 out << "" << endl;
2824 out << "parArch=`grep -Ei \"Cannot Build the PAR Archive\" stderr`" << endl;
2825 out << "segViol=`grep -Ei \"Segmentation violation\" stderr`" << endl;
2826 out << "segFault=`grep -Ei \"Segmentation fault\" stderr`" << endl;
2827 out << "" << endl;
2828
2829 out << "if [ ! -f stderr ] ; then" << endl;
2830 out << " error=1" << endl;
2831 out << " echo \"* ########## Job not validated - no stderr ###\" " << out_stream << endl;
2832 out << " echo \"Error = $error\" " << out_stream << endl;
2833 out << "fi" << endl;
2834
2835 out << "if [ \"$parArch\" != \"\" ] ; then" << endl;
2836 out << " error=1" << endl;
2837 out << " echo \"* ########## Job not validated - PAR archive not built ###\" " << out_stream << endl;
2838 out << " echo \"$parArch\" " << out_stream << endl;
2839 out << " echo \"Error = $error\" " << out_stream << endl;
2840 out << "fi" << endl;
2841
2842 out << "if [ \"$segViol\" != \"\" ] ; then" << endl;
2843 out << " error=1" << endl;
2844 out << " echo \"* ########## Job not validated - Segment. violation ###\" " << out_stream << endl;
2845 out << " echo \"$segViol\" " << out_stream << endl;
2846 out << " echo \"Error = $error\" " << out_stream << endl;
2847 out << "fi" << endl;
2848
2849 out << "if [ \"$segFault\" != \"\" ] ; then" << endl;
2850 out << " error=1" << endl;
2851 out << " echo \"* ########## Job not validated - Segment. fault ###\" " << out_stream << endl;
2852 out << " echo \"$segFault\" " << out_stream << endl;
2853 out << " echo \"Error = $error\" " << out_stream << endl;
2854 out << "fi" << endl;
2855
2856 // Part dedicated to the specific analyses running into the train
2857
c57f56b7 2858 TObjArray *arr = fOutputFiles.Tokenize(" ");
2859 TIter next1(arr);
2860 TString output_file;
5b9b4998 2861 AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
2862 TString extra = mgr->GetExtraFiles();
c57f56b7 2863 while ((os=(TObjString*)next1())) {
2864 output_file = os->GetString();
2865 Int_t index = output_file.Index("@");
2866 if (index > 0) output_file.Remove(index);
0f389141 2867 if (merge && fMergeExcludes.Contains(output_file)) continue;
5b9b4998 2868 if (extra.Contains(output_file)) continue;
c57f56b7 2869 out << "if ! [ -f " << output_file.Data() << " ] ; then" << endl;
2870 out << " error=1" << endl;
2871 out << " echo \"Output file(s) not found. Job FAILED !\"" << out_stream << endl;
2872 out << " echo \"Output file(s) not found. Job FAILED !\" >> stderr" << endl;
2873 out << "fi" << endl;
2874 }
2875 delete arr;
f866cba5 2876 if (!merge) {
2877 out << "if ! [ -f outputs_valid ] ; then" << endl;
2878 out << " error=1" << endl;
2879 out << " echo \"Output files were not validated by the analysis manager\" >> stdout" << endl;
2880 out << " echo \"Output files were not validated by the analysis manager\" >> stderr" << endl;
2881 out << "fi" << endl;
2882 }
923e2ca5 2883
c57f56b7 2884 out << "if [ $error = 0 ] ; then" << endl;
2885 out << " echo \"* ---------------- Job Validated ------------------*\"" << out_stream << endl;
2886 out << "fi" << endl;
2887
2888 out << "echo \"* ----------------------------------------------------*\"" << out_stream << endl;
2889 out << "echo \"*******************************************************\"" << out_stream << endl;
2890 out << "cd -" << endl;
2891 out << "exit $error" << endl;
2892 }
2893 Bool_t copy = kTRUE;
2894 if (TestBit(AliAnalysisGrid::kOffline) || TestBit(AliAnalysisGrid::kTest)) copy = kFALSE;
2895 if (copy) {
2896 CdWork();
2897 TString workdir = gGrid->GetHomeDirectory();
2898 workdir += fGridWorkingDir;
0d5d317c 2899 Info("CreateJDL", "\n##### Copying validation script <%s> to your AliEn working space", validationScript.Data());
2900 if (FileExists(validationScript)) gGrid->Rm(validationScript);
2901 TFile::Cp(Form("file:%s",validationScript.Data()), Form("alien://%s/%s", workdir.Data(),validationScript.Data()));
c57f56b7 2902 }
2903}